Starting phenix.real_space_refine on Tue Feb 3 12:57:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jd7_61383/02_2026/9jd7_61383.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jd7_61383/02_2026/9jd7_61383.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.57 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9jd7_61383/02_2026/9jd7_61383.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jd7_61383/02_2026/9jd7_61383.map" model { file = "/net/cci-nas-00/data/ceres_data/9jd7_61383/02_2026/9jd7_61383.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jd7_61383/02_2026/9jd7_61383.cif" } resolution = 3.57 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= 0.001 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 3 Type Number sf(0) Gaussians C 1647 2.51 5 N 450 2.21 5 O 540 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 2637 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 435 Classifications: {'peptide': 62} Link IDs: {'TRANS': 61} Chain: "B" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 444 Classifications: {'peptide': 63} Link IDs: {'TRANS': 62} Restraints were copied for chains: C, E, D, F Time building chain proxies: 0.60, per 1000 atoms: 0.23 Number of scatterers: 2637 At special positions: 0 Unit cell: (108.73, 87.98, 31.54, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 540 8.00 N 450 7.00 C 1647 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.24 Conformation dependent library (CDL) restraints added in 123.9 milliseconds 726 Ramachandran restraints generated. 363 Oldfield, 0 Emsley, 363 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 654 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 15 sheets defined 0.0% alpha, 33.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.14 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'C' and resid 39 through 40 removed outlier: 6.181A pdb=" N TYR A 39 " --> pdb=" O VAL E 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 43 through 46 removed outlier: 6.768A pdb=" N LYS A 43 " --> pdb=" O THR C 44 " (cutoff:3.500A) removed outlier: 7.886A pdb=" N GLU C 46 " --> pdb=" O LYS A 43 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N LYS A 45 " --> pdb=" O GLU C 46 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 49 through 57 removed outlier: 6.856A pdb=" N HIS C 50 " --> pdb=" O VAL A 49 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N ASP A 51 " --> pdb=" O HIS C 50 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N HIS A 50 " --> pdb=" O ASP E 51 " (cutoff:3.500A) removed outlier: 8.214A pdb=" N THR E 53 " --> pdb=" O HIS A 50 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N VAL A 52 " --> pdb=" O THR E 53 " (cutoff:3.500A) removed outlier: 8.025A pdb=" N VAL E 55 " --> pdb=" O VAL A 52 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N THR A 54 " --> pdb=" O VAL E 55 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N GLU E 57 " --> pdb=" O THR A 54 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ALA A 56 " --> pdb=" O GLU E 57 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 60 through 62 removed outlier: 6.531A pdb=" N LYS A 60 " --> pdb=" O GLU C 61 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 75 through 82 removed outlier: 6.846A pdb=" N ALA A 76 " --> pdb=" O THR C 75 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N VAL C 77 " --> pdb=" O ALA A 76 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N ALA A 78 " --> pdb=" O VAL C 77 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N GLN C 79 " --> pdb=" O ALA A 78 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N LYS A 80 " --> pdb=" O GLN C 79 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N THR E 81 " --> pdb=" O LYS A 80 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N VAL A 82 " --> pdb=" O THR E 81 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 88 through 89 removed outlier: 6.602A pdb=" N ILE A 88 " --> pdb=" O ALA E 89 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 94 through 96 removed outlier: 6.387A pdb=" N VAL A 95 " --> pdb=" O LYS C 96 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 38 through 41 removed outlier: 8.647A pdb=" N LEU B 38 " --> pdb=" O TYR D 39 " (cutoff:3.500A) removed outlier: 8.894A pdb=" N GLY D 41 " --> pdb=" O LEU B 38 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N VAL B 40 " --> pdb=" O GLY D 41 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N TYR B 39 " --> pdb=" O LEU F 38 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N VAL F 40 " --> pdb=" O TYR B 39 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 44 through 46 removed outlier: 6.306A pdb=" N THR B 44 " --> pdb=" O LYS D 45 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N LYS B 45 " --> pdb=" O GLU F 46 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'D' and resid 53 through 55 removed outlier: 6.447A pdb=" N THR B 54 " --> pdb=" O VAL D 55 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 60 through 64 removed outlier: 6.515A pdb=" N LYS B 60 " --> pdb=" O GLU F 61 " (cutoff:3.500A) removed outlier: 8.379A pdb=" N VAL F 63 " --> pdb=" O LYS B 60 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N GLN B 62 " --> pdb=" O VAL F 63 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 69 through 71 removed outlier: 6.842A pdb=" N VAL B 70 " --> pdb=" O VAL D 71 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 75 through 78 removed outlier: 6.356A pdb=" N ALA B 76 " --> pdb=" O VAL D 77 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 82 through 83 removed outlier: 6.269A pdb=" N VAL B 82 " --> pdb=" O GLU F 83 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 88 through 89 removed outlier: 6.640A pdb=" N ILE B 88 " --> pdb=" O ALA D 89 " (cutoff:3.500A) 36 hydrogen bonds defined for protein. 108 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.37 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: 1.22 - 1.28: 468 1.28 - 1.35: 402 1.35 - 1.41: 103 1.41 - 1.48: 434 1.48 - 1.54: 1242 Bond restraints: 2649 Sorted by residual: bond pdb=" CA GLN D 79 " pdb=" CB GLN D 79 " ideal model delta sigma weight residual 1.535 1.509 0.026 1.71e-02 3.42e+03 2.32e+00 bond pdb=" CA GLN B 79 " pdb=" CB GLN B 79 " ideal model delta sigma weight residual 1.535 1.509 0.026 1.71e-02 3.42e+03 2.32e+00 bond pdb=" CA GLN F 79 " pdb=" CB GLN F 79 " ideal model delta sigma weight residual 1.535 1.509 0.026 1.71e-02 3.42e+03 2.29e+00 bond pdb=" CB VAL D 52 " pdb=" CG2 VAL D 52 " ideal model delta sigma weight residual 1.521 1.487 0.034 3.30e-02 9.18e+02 1.08e+00 bond pdb=" N LYS B 43 " pdb=" CA LYS B 43 " ideal model delta sigma weight residual 1.464 1.451 0.013 1.25e-02 6.40e+03 1.07e+00 ... (remaining 2644 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.14: 3165 1.14 - 2.28: 343 2.28 - 3.43: 56 3.43 - 4.57: 12 4.57 - 5.71: 12 Bond angle restraints: 3588 Sorted by residual: angle pdb=" N TYR F 39 " pdb=" CA TYR F 39 " pdb=" C TYR F 39 " ideal model delta sigma weight residual 109.07 103.94 5.13 1.61e+00 3.86e-01 1.01e+01 angle pdb=" N TYR D 39 " pdb=" CA TYR D 39 " pdb=" C TYR D 39 " ideal model delta sigma weight residual 109.07 103.95 5.12 1.61e+00 3.86e-01 1.01e+01 angle pdb=" N TYR B 39 " pdb=" CA TYR B 39 " pdb=" C TYR B 39 " ideal model delta sigma weight residual 109.07 103.96 5.11 1.61e+00 3.86e-01 1.01e+01 angle pdb=" C VAL C 49 " pdb=" N HIS C 50 " pdb=" CA HIS C 50 " ideal model delta sigma weight residual 121.87 116.68 5.19 1.64e+00 3.72e-01 1.00e+01 angle pdb=" C VAL A 49 " pdb=" N HIS A 50 " pdb=" CA HIS A 50 " ideal model delta sigma weight residual 121.87 116.71 5.16 1.64e+00 3.72e-01 9.91e+00 ... (remaining 3583 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.92: 1314 11.92 - 23.84: 174 23.84 - 35.76: 54 35.76 - 47.68: 15 47.68 - 59.61: 3 Dihedral angle restraints: 1560 sinusoidal: 531 harmonic: 1029 Sorted by residual: 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 -163.43 -16.57 0 5.00e+00 4.00e-02 1.10e+01 dihedral pdb=" CA GLY B 41 " pdb=" C GLY B 41 " pdb=" N SER B 42 " pdb=" CA SER B 42 " ideal model delta harmonic sigma weight residual -180.00 -163.45 -16.55 0 5.00e+00 4.00e-02 1.10e+01 dihedral pdb=" CA GLY D 41 " pdb=" C GLY D 41 " pdb=" N SER D 42 " pdb=" CA SER D 42 " ideal model delta harmonic sigma weight residual -180.00 -163.46 -16.54 0 5.00e+00 4.00e-02 1.09e+01 ... (remaining 1557 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 212 0.034 - 0.067: 151 0.067 - 0.101: 59 0.101 - 0.135: 42 0.135 - 0.168: 13 Chirality restraints: 477 Sorted by residual: chirality pdb=" CA TYR B 39 " pdb=" N TYR B 39 " pdb=" C TYR B 39 " pdb=" CB TYR B 39 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.10e-01 chirality pdb=" CA TYR D 39 " pdb=" N TYR D 39 " pdb=" C TYR D 39 " pdb=" CB TYR D 39 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.08e-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 2.61 -0.17 2.00e-01 2.50e+01 7.07e-01 ... (remaining 474 not shown) Planarity restraints: 444 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS D 50 " -0.012 2.00e-02 2.50e+03 1.01e-02 1.52e+00 pdb=" CG HIS D 50 " 0.021 2.00e-02 2.50e+03 pdb=" ND1 HIS D 50 " 0.000 2.00e-02 2.50e+03 pdb=" CD2 HIS D 50 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 HIS D 50 " -0.004 2.00e-02 2.50e+03 pdb=" NE2 HIS D 50 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS B 50 " -0.012 2.00e-02 2.50e+03 9.85e-03 1.46e+00 pdb=" CG HIS B 50 " 0.020 2.00e-02 2.50e+03 pdb=" ND1 HIS B 50 " 0.000 2.00e-02 2.50e+03 pdb=" CD2 HIS B 50 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 HIS B 50 " -0.004 2.00e-02 2.50e+03 pdb=" NE2 HIS B 50 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS F 50 " -0.012 2.00e-02 2.50e+03 9.79e-03 1.44e+00 pdb=" CG HIS F 50 " 0.020 2.00e-02 2.50e+03 pdb=" ND1 HIS F 50 " 0.000 2.00e-02 2.50e+03 pdb=" CD2 HIS F 50 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 HIS F 50 " -0.004 2.00e-02 2.50e+03 pdb=" NE2 HIS F 50 " -0.004 2.00e-02 2.50e+03 ... (remaining 441 not shown) Histogram of nonbonded interaction distances: 2.36 - 2.87: 1002 2.87 - 3.38: 2292 3.38 - 3.88: 3908 3.88 - 4.39: 4195 4.39 - 4.90: 8795 Nonbonded interactions: 20192 Sorted by model distance: nonbonded pdb=" ND1 HIS E 50 " pdb=" OD2 ASP E 51 " model vdw 2.359 3.120 nonbonded pdb=" ND1 HIS A 50 " pdb=" OD2 ASP A 51 " model vdw 2.359 3.120 nonbonded pdb=" ND1 HIS C 50 " pdb=" OD2 ASP C 51 " model vdw 2.359 3.120 nonbonded pdb=" OE1 GLU B 46 " pdb=" NZ LYS F 80 " model vdw 2.363 3.120 nonbonded pdb=" NZ LYS B 80 " pdb=" OE1 GLU D 46 " model vdw 2.423 3.120 ... (remaining 20187 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 'C' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 1.580 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: 0.000 Set scattering table: 0.030 Process input model: 4.830 Find NCS groups from input model: 0.020 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:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7460 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 : 0.008 0.034 2649 Z= 0.379 Angle : 0.830 5.709 3588 Z= 0.490 Chirality : 0.060 0.168 477 Planarity : 0.003 0.010 444 Dihedral : 12.645 59.606 906 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.44 % Favored : 92.56 % Rotamer: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % 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: -5.24 (0.23), residues: 363 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.98 (0.18), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.003 0.001 TYR C 39 PHE 0.010 0.002 PHE D 94 HIS 0.007 0.004 HIS D 50 Details of bonding type rmsd covalent geometry : bond 0.00753 ( 2649) covalent geometry : angle 0.83013 ( 3588) hydrogen bonds : bond 0.15031 ( 36) hydrogen bonds : angle 8.11672 ( 108) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 726 Ramachandran restraints generated. 363 Oldfield, 0 Emsley, 363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 726 Ramachandran restraints generated. 363 Oldfield, 0 Emsley, 363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 26 time to evaluate : 0.097 Fit side-chains REVERT: A 58 LYS cc_start: 0.6761 (tttt) cc_final: 0.6100 (mttt) REVERT: A 62 GLN cc_start: 0.7561 (mt0) cc_final: 0.6735 (tm-30) REVERT: A 83 GLU cc_start: 0.7179 (mp0) cc_final: 0.6696 (mp0) REVERT: C 46 GLU cc_start: 0.7882 (mt-10) cc_final: 0.7645 (mt-10) REVERT: C 83 GLU cc_start: 0.7501 (mp0) cc_final: 0.6974 (mp0) REVERT: D 51 ASP cc_start: 0.8760 (m-30) cc_final: 0.8558 (m-30) REVERT: E 58 LYS cc_start: 0.7272 (tttt) cc_final: 0.6476 (mttt) outliers start: 0 outliers final: 0 residues processed: 26 average time/residue: 0.0851 time to fit residues: 2.6642 Evaluate side-chains 24 residues out of total 279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.098 ------------------------------------------------------------------------------- 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: 6.9990 chunk 26 optimal weight: 20.0000 chunk 2 optimal weight: 8.9990 chunk 16 optimal weight: 5.9990 chunk 32 optimal weight: 6.9990 chunk 31 optimal weight: 3.9990 chunk 25 optimal weight: 4.9990 chunk 19 optimal weight: 0.9990 chunk 30 optimal weight: 9.9990 chunk 22 optimal weight: 0.9990 chunk 13 optimal weight: 3.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.132981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.112932 restraints weight = 3278.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.115759 restraints weight = 1537.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.117550 restraints weight = 981.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.118652 restraints weight = 753.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.119262 restraints weight = 642.078| |-----------------------------------------------------------------------------| r_work (final): 0.4028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.1514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 2649 Z= 0.170 Angle : 0.538 4.558 3588 Z= 0.304 Chirality : 0.053 0.157 477 Planarity : 0.002 0.007 444 Dihedral : 4.897 11.185 375 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 2.15 % Allowed : 8.96 % Favored : 88.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.69 (0.24), residues: 363 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.57 (0.19), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.010 0.002 TYR A 39 PHE 0.006 0.001 PHE D 94 HIS 0.006 0.003 HIS F 50 Details of bonding type rmsd covalent geometry : bond 0.00357 ( 2649) covalent geometry : angle 0.53752 ( 3588) hydrogen bonds : bond 0.01341 ( 36) hydrogen bonds : angle 4.84047 ( 108) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 726 Ramachandran restraints generated. 363 Oldfield, 0 Emsley, 363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 726 Ramachandran restraints generated. 363 Oldfield, 0 Emsley, 363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 23 time to evaluate : 0.098 Fit side-chains REVERT: A 58 LYS cc_start: 0.7437 (tttt) cc_final: 0.6829 (mttt) REVERT: A 60 LYS cc_start: 0.7659 (mttt) cc_final: 0.7253 (tttp) REVERT: A 83 GLU cc_start: 0.7610 (mp0) cc_final: 0.7138 (mp0) REVERT: C 60 LYS cc_start: 0.7891 (mttt) cc_final: 0.7498 (mptt) REVERT: C 83 GLU cc_start: 0.7775 (mp0) cc_final: 0.7461 (mp0) REVERT: E 58 LYS cc_start: 0.7649 (tttt) cc_final: 0.6934 (mttt) outliers start: 6 outliers final: 5 residues processed: 27 average time/residue: 0.1083 time to fit residues: 3.3735 Evaluate side-chains 27 residues out of total 279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 22 time to evaluate : 0.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain F residue 48 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 6 optimal weight: 10.0000 chunk 33 optimal weight: 10.0000 chunk 4 optimal weight: 10.0000 chunk 8 optimal weight: 6.9990 chunk 31 optimal weight: 9.9990 chunk 2 optimal weight: 30.0000 chunk 14 optimal weight: 5.9990 chunk 22 optimal weight: 0.8980 chunk 35 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.133131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.111692 restraints weight = 3246.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.114613 restraints weight = 1582.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.116370 restraints weight = 1018.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.117583 restraints weight = 784.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.118242 restraints weight = 663.762| |-----------------------------------------------------------------------------| r_work (final): 0.4042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.1898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 2649 Z= 0.127 Angle : 0.477 3.857 3588 Z= 0.269 Chirality : 0.051 0.144 477 Planarity : 0.001 0.006 444 Dihedral : 4.412 10.140 375 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 2.51 % Allowed : 10.39 % Favored : 87.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.16 (0.28), residues: 363 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.16 (0.21), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.007 0.002 TYR A 39 PHE 0.005 0.001 PHE D 94 HIS 0.004 0.002 HIS D 50 Details of bonding type rmsd covalent geometry : bond 0.00269 ( 2649) covalent geometry : angle 0.47687 ( 3588) hydrogen bonds : bond 0.01059 ( 36) hydrogen bonds : angle 4.26725 ( 108) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 726 Ramachandran restraints generated. 363 Oldfield, 0 Emsley, 363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 726 Ramachandran restraints generated. 363 Oldfield, 0 Emsley, 363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 26 time to evaluate : 0.101 Fit side-chains REVERT: A 58 LYS cc_start: 0.7273 (tttt) cc_final: 0.6691 (mttt) REVERT: A 60 LYS cc_start: 0.7629 (mttt) cc_final: 0.7205 (tttp) REVERT: A 83 GLU cc_start: 0.7513 (mp0) cc_final: 0.7070 (mp0) REVERT: C 60 LYS cc_start: 0.7859 (mttt) cc_final: 0.7416 (mptt) REVERT: C 83 GLU cc_start: 0.7610 (mp0) cc_final: 0.7354 (mp0) REVERT: E 58 LYS cc_start: 0.7591 (tttt) cc_final: 0.7137 (mttt) REVERT: E 60 LYS cc_start: 0.7380 (mttt) cc_final: 0.6944 (mptt) REVERT: E 83 GLU cc_start: 0.7634 (mp0) cc_final: 0.7386 (mp0) outliers start: 7 outliers final: 4 residues processed: 32 average time/residue: 0.1022 time to fit residues: 3.7479 Evaluate side-chains 29 residues out of total 279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 25 time to evaluate : 0.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain B residue 99 GLN Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain E residue 48 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 6 optimal weight: 10.0000 chunk 22 optimal weight: 10.0000 chunk 18 optimal weight: 8.9990 chunk 12 optimal weight: 9.9990 chunk 21 optimal weight: 0.0970 chunk 14 optimal weight: 8.9990 chunk 15 optimal weight: 9.9990 chunk 24 optimal weight: 10.0000 chunk 7 optimal weight: 5.9990 chunk 34 optimal weight: 4.9990 chunk 16 optimal weight: 8.9990 overall best weight: 5.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.126605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.106098 restraints weight = 3353.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.108843 restraints weight = 1623.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.110635 restraints weight = 1054.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.111638 restraints weight = 814.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.112211 restraints weight = 702.988| |-----------------------------------------------------------------------------| r_work (final): 0.3904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.2052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 2649 Z= 0.306 Angle : 0.649 4.639 3588 Z= 0.374 Chirality : 0.056 0.164 477 Planarity : 0.003 0.009 444 Dihedral : 5.436 16.778 375 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.99 % Favored : 92.01 % Rotamer: Outliers : 2.87 % Allowed : 11.11 % Favored : 86.02 % 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: -4.30 (0.27), residues: 363 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.27 (0.21), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.015 0.003 TYR C 39 PHE 0.010 0.002 PHE F 94 HIS 0.008 0.004 HIS F 50 Details of bonding type rmsd covalent geometry : bond 0.00649 ( 2649) covalent geometry : angle 0.64887 ( 3588) hydrogen bonds : bond 0.01547 ( 36) hydrogen bonds : angle 4.37987 ( 108) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 726 Ramachandran restraints generated. 363 Oldfield, 0 Emsley, 363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 726 Ramachandran restraints generated. 363 Oldfield, 0 Emsley, 363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 29 time to evaluate : 0.114 Fit side-chains REVERT: A 58 LYS cc_start: 0.7296 (tttt) cc_final: 0.6662 (mtmt) REVERT: A 60 LYS cc_start: 0.7599 (mttt) cc_final: 0.7181 (tttp) REVERT: A 83 GLU cc_start: 0.7661 (mp0) cc_final: 0.7359 (mp0) REVERT: C 60 LYS cc_start: 0.7940 (mttt) cc_final: 0.7455 (mptt) REVERT: C 83 GLU cc_start: 0.7762 (mp0) cc_final: 0.7434 (mp0) REVERT: E 58 LYS cc_start: 0.7520 (tttt) cc_final: 0.7021 (mttt) REVERT: E 60 LYS cc_start: 0.7411 (mttt) cc_final: 0.6942 (mptt) REVERT: F 72 THR cc_start: 0.8071 (m) cc_final: 0.7679 (p) REVERT: F 96 LYS cc_start: 0.7602 (tttt) cc_final: 0.7144 (ttmt) REVERT: F 99 GLN cc_start: 0.5657 (OUTLIER) cc_final: 0.5388 (pt0) outliers start: 8 outliers final: 6 residues processed: 34 average time/residue: 0.0890 time to fit residues: 3.5250 Evaluate side-chains 36 residues out of total 279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 29 time to evaluate : 0.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 99 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 22 optimal weight: 0.1980 chunk 17 optimal weight: 0.0570 chunk 5 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 1 optimal weight: 0.9990 chunk 29 optimal weight: 4.9990 chunk 3 optimal weight: 7.9990 chunk 9 optimal weight: 10.0000 chunk 16 optimal weight: 7.9990 chunk 19 optimal weight: 6.9990 chunk 4 optimal weight: 2.9990 overall best weight: 1.8504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.136375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.115235 restraints weight = 3193.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.118346 restraints weight = 1442.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.120296 restraints weight = 894.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.121454 restraints weight = 673.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.122331 restraints weight = 569.382| |-----------------------------------------------------------------------------| r_work (final): 0.4077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.2368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 2649 Z= 0.110 Angle : 0.456 3.443 3588 Z= 0.259 Chirality : 0.051 0.144 477 Planarity : 0.001 0.007 444 Dihedral : 4.321 10.610 375 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 2.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 1.08 % Allowed : 13.62 % Favored : 85.30 % 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: -3.96 (0.29), residues: 363 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.01 (0.22), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.005 0.001 TYR C 39 PHE 0.005 0.001 PHE D 94 HIS 0.004 0.002 HIS B 50 Details of bonding type rmsd covalent geometry : bond 0.00229 ( 2649) covalent geometry : angle 0.45623 ( 3588) hydrogen bonds : bond 0.00964 ( 36) hydrogen bonds : angle 3.85361 ( 108) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 726 Ramachandran restraints generated. 363 Oldfield, 0 Emsley, 363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 726 Ramachandran restraints generated. 363 Oldfield, 0 Emsley, 363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 29 time to evaluate : 0.101 Fit side-chains REVERT: A 58 LYS cc_start: 0.7306 (tttt) cc_final: 0.6665 (mttt) REVERT: A 60 LYS cc_start: 0.7538 (mttt) cc_final: 0.7085 (tttp) REVERT: A 83 GLU cc_start: 0.7552 (mp0) cc_final: 0.7117 (mp0) REVERT: C 60 LYS cc_start: 0.7907 (mttt) cc_final: 0.7413 (mptt) REVERT: C 83 GLU cc_start: 0.7571 (mp0) cc_final: 0.7302 (mp0) REVERT: C 97 LYS cc_start: 0.8344 (mttm) cc_final: 0.7762 (mmtp) REVERT: E 58 LYS cc_start: 0.7516 (tttt) cc_final: 0.7013 (mttt) REVERT: E 60 LYS cc_start: 0.7364 (mttt) cc_final: 0.6876 (mptt) REVERT: E 83 GLU cc_start: 0.7703 (mp0) cc_final: 0.7361 (mp0) outliers start: 3 outliers final: 3 residues processed: 32 average time/residue: 0.0938 time to fit residues: 3.4859 Evaluate side-chains 31 residues out of total 279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 28 time to evaluate : 0.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain E residue 48 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 17 optimal weight: 0.8980 chunk 9 optimal weight: 10.0000 chunk 16 optimal weight: 10.0000 chunk 14 optimal weight: 0.3980 chunk 35 optimal weight: 0.0870 chunk 26 optimal weight: 8.9990 chunk 13 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 chunk 2 optimal weight: 9.9990 chunk 32 optimal weight: 0.1980 chunk 8 optimal weight: 6.9990 overall best weight: 0.5160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 79 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4354 r_free = 0.4354 target = 0.146680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.126024 restraints weight = 3082.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.129148 restraints weight = 1540.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.131113 restraints weight = 989.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.132358 restraints weight = 746.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.133124 restraints weight = 626.345| |-----------------------------------------------------------------------------| r_work (final): 0.4240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.2854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.012 2649 Z= 0.057 Angle : 0.365 2.607 3588 Z= 0.209 Chirality : 0.050 0.128 477 Planarity : 0.001 0.006 444 Dihedral : 3.561 10.409 375 Min Nonbonded Distance : 2.637 Molprobity Statistics. All-atom Clashscore : 1.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 0.36 % Allowed : 13.62 % Favored : 86.02 % 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: -3.29 (0.33), residues: 363 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.50 (0.25), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.002 0.000 TYR C 39 PHE 0.003 0.001 PHE B 94 HIS 0.003 0.001 HIS B 50 Details of bonding type rmsd covalent geometry : bond 0.00111 ( 2649) covalent geometry : angle 0.36508 ( 3588) hydrogen bonds : bond 0.00871 ( 36) hydrogen bonds : angle 3.55838 ( 108) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 726 Ramachandran restraints generated. 363 Oldfield, 0 Emsley, 363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 726 Ramachandran restraints generated. 363 Oldfield, 0 Emsley, 363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 26 time to evaluate : 0.097 Fit side-chains REVERT: A 58 LYS cc_start: 0.7445 (tttt) cc_final: 0.6976 (mtmt) REVERT: A 60 LYS cc_start: 0.7673 (mttt) cc_final: 0.7190 (tttm) REVERT: A 83 GLU cc_start: 0.7361 (mp0) cc_final: 0.6955 (mp0) REVERT: C 60 LYS cc_start: 0.7962 (mttt) cc_final: 0.7552 (tttp) REVERT: C 83 GLU cc_start: 0.7257 (mp0) cc_final: 0.6953 (mp0) REVERT: E 60 LYS cc_start: 0.7339 (mttt) cc_final: 0.6888 (tttp) outliers start: 1 outliers final: 0 residues processed: 27 average time/residue: 0.1150 time to fit residues: 3.5475 Evaluate side-chains 24 residues out of total 279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 21 optimal weight: 10.0000 chunk 12 optimal weight: 10.0000 chunk 22 optimal weight: 1.9990 chunk 34 optimal weight: 5.9990 chunk 26 optimal weight: 20.0000 chunk 30 optimal weight: 9.9990 chunk 13 optimal weight: 0.9990 chunk 29 optimal weight: 10.0000 chunk 23 optimal weight: 9.9990 chunk 25 optimal weight: 9.9990 chunk 9 optimal weight: 3.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.130044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.109385 restraints weight = 3296.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.112036 restraints weight = 1611.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.113852 restraints weight = 1054.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.114958 restraints weight = 809.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.115638 restraints weight = 690.598| |-----------------------------------------------------------------------------| r_work (final): 0.3977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.2577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 2649 Z= 0.241 Angle : 0.557 3.963 3588 Z= 0.321 Chirality : 0.054 0.156 477 Planarity : 0.002 0.009 444 Dihedral : 4.649 13.108 375 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.89 % Favored : 93.11 % Rotamer: Outliers : 1.43 % Allowed : 13.98 % Favored : 84.59 % 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: -3.32 (0.33), residues: 363 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.53 (0.25), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.010 0.003 TYR C 39 PHE 0.008 0.002 PHE F 94 HIS 0.007 0.004 HIS F 50 Details of bonding type rmsd covalent geometry : bond 0.00515 ( 2649) covalent geometry : angle 0.55677 ( 3588) hydrogen bonds : bond 0.01237 ( 36) hydrogen bonds : angle 3.76996 ( 108) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 726 Ramachandran restraints generated. 363 Oldfield, 0 Emsley, 363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 726 Ramachandran restraints generated. 363 Oldfield, 0 Emsley, 363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 28 time to evaluate : 0.104 Fit side-chains REVERT: A 58 LYS cc_start: 0.7262 (tttt) cc_final: 0.6660 (mttt) REVERT: A 60 LYS cc_start: 0.7579 (mttt) cc_final: 0.7146 (tttp) REVERT: A 83 GLU cc_start: 0.7641 (mp0) cc_final: 0.7417 (mp0) REVERT: C 60 LYS cc_start: 0.7957 (mttt) cc_final: 0.7494 (tttp) REVERT: E 58 LYS cc_start: 0.7450 (tttt) cc_final: 0.7024 (mttt) REVERT: E 60 LYS cc_start: 0.7315 (mttt) cc_final: 0.6929 (mptt) REVERT: F 96 LYS cc_start: 0.7533 (tttt) cc_final: 0.7135 (ttmt) outliers start: 4 outliers final: 4 residues processed: 31 average time/residue: 0.1038 time to fit residues: 3.7053 Evaluate side-chains 32 residues out of total 279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 28 time to evaluate : 0.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain E residue 48 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 25 optimal weight: 5.9990 chunk 13 optimal weight: 4.9990 chunk 4 optimal weight: 9.9990 chunk 22 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 chunk 8 optimal weight: 10.0000 chunk 28 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 33 optimal weight: 0.0270 chunk 35 optimal weight: 7.9990 chunk 5 optimal weight: 9.9990 overall best weight: 2.5244 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.135303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.114361 restraints weight = 3224.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.117332 restraints weight = 1528.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.119189 restraints weight = 970.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.120290 restraints weight = 740.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.121086 restraints weight = 631.090| |-----------------------------------------------------------------------------| r_work (final): 0.4048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.2750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 2649 Z= 0.141 Angle : 0.477 4.217 3588 Z= 0.272 Chirality : 0.051 0.145 477 Planarity : 0.002 0.006 444 Dihedral : 4.274 10.429 375 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 2.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 0.36 % Allowed : 15.41 % Favored : 84.23 % 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: -3.18 (0.34), residues: 363 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.41 (0.26), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.006 0.001 TYR C 39 PHE 0.004 0.001 PHE D 94 HIS 0.005 0.002 HIS B 50 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 2649) covalent geometry : angle 0.47674 ( 3588) hydrogen bonds : bond 0.01014 ( 36) hydrogen bonds : angle 3.64928 ( 108) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 726 Ramachandran restraints generated. 363 Oldfield, 0 Emsley, 363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 726 Ramachandran restraints generated. 363 Oldfield, 0 Emsley, 363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 28 time to evaluate : 0.099 Fit side-chains REVERT: A 58 LYS cc_start: 0.7282 (tttt) cc_final: 0.6669 (mttt) REVERT: A 60 LYS cc_start: 0.7555 (mttt) cc_final: 0.7055 (tttm) REVERT: A 83 GLU cc_start: 0.7586 (mp0) cc_final: 0.7282 (mp0) REVERT: C 60 LYS cc_start: 0.7944 (mttt) cc_final: 0.7503 (tttp) REVERT: E 58 LYS cc_start: 0.7488 (tttt) cc_final: 0.7177 (mtmt) REVERT: E 60 LYS cc_start: 0.7321 (mttt) cc_final: 0.6927 (mptt) outliers start: 1 outliers final: 1 residues processed: 29 average time/residue: 0.1009 time to fit residues: 3.3867 Evaluate side-chains 29 residues out of total 279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 28 time to evaluate : 0.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 48 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 28 optimal weight: 0.3980 chunk 15 optimal weight: 10.0000 chunk 22 optimal weight: 0.9990 chunk 5 optimal weight: 8.9990 chunk 18 optimal weight: 5.9990 chunk 6 optimal weight: 9.9990 chunk 9 optimal weight: 10.0000 chunk 33 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 31 optimal weight: 9.9990 chunk 10 optimal weight: 4.9990 overall best weight: 2.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.134271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.113294 restraints weight = 3316.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.116238 restraints weight = 1559.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.118075 restraints weight = 986.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.119313 restraints weight = 754.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.119977 restraints weight = 636.314| |-----------------------------------------------------------------------------| r_work (final): 0.4041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.2851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 2649 Z= 0.150 Angle : 0.489 5.871 3588 Z= 0.278 Chirality : 0.051 0.147 477 Planarity : 0.002 0.020 444 Dihedral : 4.218 10.270 375 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 0.72 % Allowed : 15.05 % Favored : 84.23 % 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: -3.05 (0.36), residues: 363 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.32 (0.27), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.006 0.002 TYR C 39 PHE 0.005 0.001 PHE D 94 HIS 0.005 0.002 HIS F 50 Details of bonding type rmsd covalent geometry : bond 0.00322 ( 2649) covalent geometry : angle 0.48931 ( 3588) hydrogen bonds : bond 0.00998 ( 36) hydrogen bonds : angle 3.58388 ( 108) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 726 Ramachandran restraints generated. 363 Oldfield, 0 Emsley, 363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 726 Ramachandran restraints generated. 363 Oldfield, 0 Emsley, 363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 28 time to evaluate : 0.102 Fit side-chains revert: symmetry clash REVERT: A 58 LYS cc_start: 0.7253 (tttt) cc_final: 0.6656 (mttt) REVERT: A 83 GLU cc_start: 0.7435 (mp0) cc_final: 0.7067 (mp0) REVERT: C 60 LYS cc_start: 0.8028 (mttt) cc_final: 0.7546 (tttp) REVERT: E 58 LYS cc_start: 0.7471 (tttt) cc_final: 0.6933 (mttt) REVERT: E 60 LYS cc_start: 0.7295 (mttt) cc_final: 0.6873 (mptt) REVERT: E 83 GLU cc_start: 0.7727 (mp0) cc_final: 0.7422 (mp0) outliers start: 2 outliers final: 2 residues processed: 30 average time/residue: 0.0969 time to fit residues: 3.3783 Evaluate side-chains 30 residues out of total 279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 28 time to evaluate : 0.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain E residue 48 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 13 optimal weight: 1.9990 chunk 24 optimal weight: 10.0000 chunk 7 optimal weight: 10.0000 chunk 35 optimal weight: 6.9990 chunk 19 optimal weight: 8.9990 chunk 30 optimal weight: 0.0370 chunk 4 optimal weight: 9.9990 chunk 20 optimal weight: 0.1980 chunk 15 optimal weight: 9.9990 chunk 23 optimal weight: 9.9990 chunk 14 optimal weight: 6.9990 overall best weight: 3.2464 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.132424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.111197 restraints weight = 3308.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.114276 restraints weight = 1488.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.116222 restraints weight = 920.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.117444 restraints weight = 690.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.118189 restraints weight = 579.966| |-----------------------------------------------------------------------------| r_work (final): 0.4017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.2864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 2649 Z= 0.178 Angle : 0.524 6.915 3588 Z= 0.298 Chirality : 0.052 0.149 477 Planarity : 0.002 0.007 444 Dihedral : 4.370 10.265 375 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.16 % Favored : 92.84 % Rotamer: Outliers : 1.08 % Allowed : 15.05 % Favored : 83.87 % 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: -3.03 (0.36), residues: 363 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.30 (0.28), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.007 0.002 TYR C 39 PHE 0.006 0.001 PHE F 94 HIS 0.005 0.003 HIS F 50 Details of bonding type rmsd covalent geometry : bond 0.00383 ( 2649) covalent geometry : angle 0.52383 ( 3588) hydrogen bonds : bond 0.01071 ( 36) hydrogen bonds : angle 3.62847 ( 108) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 726 Ramachandran restraints generated. 363 Oldfield, 0 Emsley, 363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 726 Ramachandran restraints generated. 363 Oldfield, 0 Emsley, 363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 29 time to evaluate : 0.063 Fit side-chains REVERT: A 58 LYS cc_start: 0.7248 (tttt) cc_final: 0.6676 (mttt) REVERT: A 60 LYS cc_start: 0.7504 (mttt) cc_final: 0.7126 (mptt) REVERT: C 60 LYS cc_start: 0.8027 (mttt) cc_final: 0.7529 (tttp) REVERT: E 58 LYS cc_start: 0.7460 (tttt) cc_final: 0.6919 (mttt) REVERT: E 60 LYS cc_start: 0.7203 (mttt) cc_final: 0.6756 (mptt) REVERT: E 83 GLU cc_start: 0.7779 (mp0) cc_final: 0.7577 (mp0) REVERT: F 60 LYS cc_start: 0.7968 (mttt) cc_final: 0.7609 (mttp) outliers start: 3 outliers final: 2 residues processed: 31 average time/residue: 0.0644 time to fit residues: 2.3114 Evaluate side-chains 31 residues out of total 279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 29 time to evaluate : 0.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain E residue 48 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 0 optimal weight: 10.0000 chunk 26 optimal weight: 6.9990 chunk 17 optimal weight: 7.9990 chunk 28 optimal weight: 8.9990 chunk 34 optimal weight: 8.9990 chunk 14 optimal weight: 8.9990 chunk 33 optimal weight: 0.0020 chunk 19 optimal weight: 9.9990 chunk 31 optimal weight: 10.0000 chunk 12 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 overall best weight: 4.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.129414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.108662 restraints weight = 3308.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.111349 restraints weight = 1614.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.113110 restraints weight = 1055.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.114168 restraints weight = 813.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.114780 restraints weight = 697.994| |-----------------------------------------------------------------------------| r_work (final): 0.3965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.2891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 2649 Z= 0.242 Angle : 0.587 6.036 3588 Z= 0.336 Chirality : 0.054 0.159 477 Planarity : 0.003 0.017 444 Dihedral : 4.805 13.390 375 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.82 % Favored : 91.18 % Rotamer: Outliers : 1.08 % Allowed : 15.41 % Favored : 83.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.16 (0.37), residues: 363 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.40 (0.28), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.010 0.003 TYR C 39 PHE 0.008 0.002 PHE D 94 HIS 0.007 0.003 HIS F 50 Details of bonding type rmsd covalent geometry : bond 0.00518 ( 2649) covalent geometry : angle 0.58750 ( 3588) hydrogen bonds : bond 0.01364 ( 36) hydrogen bonds : angle 3.68608 ( 108) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 631.78 seconds wall clock time: 11 minutes 33.46 seconds (693.46 seconds total)