Starting phenix.real_space_refine on Wed Sep 17 03:17:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zwk_60530/09_2025/8zwk_60530.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zwk_60530/09_2025/8zwk_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_60530/09_2025/8zwk_60530.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zwk_60530/09_2025/8zwk_60530.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8zwk_60530/09_2025/8zwk_60530.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zwk_60530/09_2025/8zwk_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-2.0-5805/lib/python3.9/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: 0.49, per 1000 atoms: 0.18 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: 0.13 Conformation dependent library (CDL) restraints added in 77.1 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.32 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: 0.24 Time building geometry restraints manager: 0.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.30: 462 1.30 - 1.38: 516 1.38 - 1.46: 365 1.46 - 1.53: 1315 1.53 - 1.61: 130 Bond restraints: 2788 Sorted by residual: bond pdb=" N GLY F 68 " pdb=" CA GLY F 68 " ideal model delta sigma weight residual 1.445 1.450 -0.006 8.30e-03 1.45e+04 4.68e-01 bond pdb=" N GLY E 68 " pdb=" CA GLY E 68 " ideal model delta sigma weight residual 1.445 1.450 -0.005 8.30e-03 1.45e+04 3.84e-01 bond pdb=" N GLY B 68 " pdb=" CA GLY B 68 " ideal model delta sigma weight residual 1.445 1.450 -0.005 8.30e-03 1.45e+04 3.63e-01 bond pdb=" N GLY C 68 " pdb=" CA GLY C 68 " ideal model delta sigma weight residual 1.445 1.449 -0.005 8.30e-03 1.45e+04 3.47e-01 bond pdb=" N GLY D 68 " pdb=" CA GLY D 68 " ideal model delta sigma weight residual 1.445 1.449 -0.005 8.30e-03 1.45e+04 3.27e-01 ... (remaining 2783 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.79: 3303 0.79 - 1.58: 355 1.58 - 2.37: 101 2.37 - 3.16: 25 3.16 - 3.95: 12 Bond angle restraints: 3796 Sorted by residual: angle pdb=" N SER D 42 " pdb=" CA SER D 42 " pdb=" C SER D 42 " ideal model delta sigma weight residual 110.80 114.75 -3.95 2.13e+00 2.20e-01 3.44e+00 angle pdb=" N SER C 42 " pdb=" CA SER C 42 " pdb=" C SER C 42 " ideal model delta sigma weight residual 110.80 114.74 -3.94 2.13e+00 2.20e-01 3.42e+00 angle pdb=" N SER B 42 " pdb=" CA SER B 42 " pdb=" C SER B 42 " ideal model delta sigma weight residual 110.80 114.74 -3.94 2.13e+00 2.20e-01 3.42e+00 angle pdb=" N SER A 42 " pdb=" CA SER A 42 " pdb=" C SER A 42 " ideal model delta sigma weight residual 110.80 114.74 -3.94 2.13e+00 2.20e-01 3.41e+00 angle pdb=" N SER E 42 " pdb=" CA SER E 42 " pdb=" C SER E 42 " ideal model delta sigma weight residual 110.80 114.72 -3.92 2.13e+00 2.20e-01 3.39e+00 ... (remaining 3791 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.43: 1550 24.43 - 48.86: 46 48.86 - 73.29: 12 73.29 - 97.71: 0 97.71 - 122.14: 6 Dihedral angle restraints: 1614 sinusoidal: 588 harmonic: 1026 Sorted by residual: dihedral pdb=" CA GLY A 41 " pdb=" C GLY A 41 " pdb=" N SER A 42 " pdb=" CA SER A 42 " ideal model delta harmonic sigma weight residual -180.00 -158.33 -21.67 0 5.00e+00 4.00e-02 1.88e+01 dihedral pdb=" CA GLY F 41 " pdb=" C GLY F 41 " pdb=" N SER F 42 " pdb=" CA SER F 42 " ideal model delta harmonic sigma weight residual -180.00 -158.33 -21.67 0 5.00e+00 4.00e-02 1.88e+01 dihedral pdb=" CA GLY E 41 " pdb=" C GLY E 41 " pdb=" N SER E 42 " pdb=" CA SER E 42 " ideal model delta harmonic sigma weight residual -180.00 -158.35 -21.65 0 5.00e+00 4.00e-02 1.88e+01 ... (remaining 1611 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 263 0.027 - 0.054: 112 0.054 - 0.081: 51 0.081 - 0.108: 37 0.108 - 0.135: 35 Chirality restraints: 498 Sorted by residual: chirality pdb=" CA VAL C 49 " pdb=" N VAL C 49 " pdb=" C VAL C 49 " pdb=" CB VAL C 49 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.13 2.00e-01 2.50e+01 4.55e-01 chirality pdb=" CA VAL D 49 " pdb=" N VAL D 49 " pdb=" C VAL D 49 " pdb=" CB VAL D 49 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.45e-01 chirality pdb=" CA VAL A 49 " pdb=" N VAL A 49 " pdb=" C VAL A 49 " pdb=" CB VAL A 49 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.40e-01 ... (remaining 495 not shown) Planarity restraints: 450 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS F 43 " -0.003 2.00e-02 2.50e+03 6.65e-03 4.42e-01 pdb=" C LYS F 43 " 0.012 2.00e-02 2.50e+03 pdb=" O LYS F 43 " -0.004 2.00e-02 2.50e+03 pdb=" N THR F 44 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS B 43 " -0.003 2.00e-02 2.50e+03 6.62e-03 4.38e-01 pdb=" C LYS B 43 " 0.011 2.00e-02 2.50e+03 pdb=" O LYS B 43 " -0.004 2.00e-02 2.50e+03 pdb=" N THR B 44 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 43 " 0.003 2.00e-02 2.50e+03 6.61e-03 4.37e-01 pdb=" C LYS A 43 " -0.011 2.00e-02 2.50e+03 pdb=" O LYS A 43 " 0.004 2.00e-02 2.50e+03 pdb=" N THR A 44 " 0.004 2.00e-02 2.50e+03 ... (remaining 447 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 527 2.78 - 3.31: 2457 3.31 - 3.84: 4297 3.84 - 4.37: 4504 4.37 - 4.90: 9330 Nonbonded interactions: 21115 Sorted by model distance: nonbonded pdb=" OE2 GLU C 46 " pdb=" NZ LYS C 80 " model vdw 2.253 3.120 nonbonded pdb=" OE2 GLU F 46 " pdb=" NZ LYS F 80 " model vdw 2.253 3.120 nonbonded pdb=" OE2 GLU D 46 " pdb=" NZ LYS D 80 " model vdw 2.253 3.120 nonbonded pdb=" OE2 GLU E 46 " pdb=" NZ LYS E 80 " model vdw 2.254 3.120 nonbonded pdb=" OE2 GLU A 46 " pdb=" NZ LYS A 80 " model vdw 2.254 3.120 ... (remaining 21110 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' selection = chain 'E' selection = chain 'B' selection = chain 'C' selection = chain 'F' } ncs_group { reference = chain 'Q' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.870 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: 0.010 Process input model: 4.100 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:0.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7486 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= 0.157 Angle : 0.602 3.950 3796 Z= 0.340 Chirality : 0.052 0.135 498 Planarity : 0.002 0.007 450 Dihedral : 16.324 122.139 966 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 13.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.20 % Favored : 91.80 % Rotamer: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren 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 covalent geometry : bond 0.00320 ( 2788) covalent geometry : angle 0.60201 ( 3796) hydrogen bonds : bond 0.21901 ( 28) hydrogen bonds : angle 8.52070 ( 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 : 0.056 Fit side-chains REVERT: A 83 GLU cc_start: 0.7922 (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: 0.0655 time to fit residues: 2.8037 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 : 0.082 ------------------------------------------------------------------------------- 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... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4424 r_free = 0.4424 target = 0.173566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.132505 restraints weight = 2836.071| |-----------------------------------------------------------------------------| r_work (start): 0.3820 rms_B_bonded: 2.43 r_work: 0.3699 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3586 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.1687 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= 0.267 Angle : 0.739 4.972 3796 Z= 0.409 Chirality : 0.054 0.133 498 Planarity : 0.003 0.010 450 Dihedral : 15.429 111.740 444 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.84 % Favored : 90.16 % Rotamer: Outliers : 7.41 % Allowed : 6.30 % Favored : 86.30 % 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 aren not related in a simple way. whole: -4.82 (0.29), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.67 (0.22), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.017 0.004 TYR E 39 PHE 0.014 0.003 PHE A 94 HIS 0.007 0.004 HIS A 50 Details of bonding type rmsd covalent geometry : bond 0.00595 ( 2788) covalent geometry : angle 0.73914 ( 3796) hydrogen bonds : bond 0.03683 ( 28) hydrogen bonds : angle 7.52514 ( 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 45 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 25 time to evaluate : 0.098 Fit side-chains REVERT: A 60 LYS cc_start: 0.6626 (mttt) cc_final: 0.6195 (mtpt) REVERT: D 60 LYS cc_start: 0.6476 (mttt) cc_final: 0.6146 (mtpt) REVERT: D 83 GLU cc_start: 0.8478 (mt-10) cc_final: 0.7825 (tp30) REVERT: E 60 LYS cc_start: 0.7256 (mttt) cc_final: 0.6822 (mtpt) REVERT: B 37 VAL cc_start: 0.6870 (OUTLIER) cc_final: 0.6504 (m) REVERT: B 60 LYS cc_start: 0.6432 (mttt) cc_final: 0.6100 (mtpt) REVERT: C 60 LYS cc_start: 0.6481 (mttt) cc_final: 0.6104 (mtpt) REVERT: F 60 LYS cc_start: 0.7214 (mttt) cc_final: 0.6846 (mtpt) REVERT: F 83 GLU cc_start: 0.8705 (mt-10) cc_final: 0.8032 (tp30) outliers start: 20 outliers final: 19 residues processed: 43 average time/residue: 0.0782 time to fit residues: 3.9098 Evaluate side-chains 45 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 25 time to evaluate : 0.098 ------------------------------------------------------------------------------- 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 75 THR 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 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 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: 4.9990 chunk 11 optimal weight: 0.9980 chunk 8 optimal weight: 7.9990 chunk 28 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 chunk 23 optimal weight: 9.9990 chunk 33 optimal weight: 0.0020 chunk 26 optimal weight: 4.9990 chunk 7 optimal weight: 5.9990 chunk 15 optimal weight: 2.9990 chunk 31 optimal weight: 5.9990 overall best weight: 2.5994 ------------------------------------------------------------------------------- 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 = 0.4470 r_free = 0.4470 target = 0.178116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.135326 restraints weight = 2742.938| |-----------------------------------------------------------------------------| r_work (start): 0.3852 rms_B_bonded: 2.44 r_work: 0.3734 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3622 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.2007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.019 2788 Z= 0.175 Angle : 0.597 4.757 3796 Z= 0.326 Chirality : 0.051 0.131 498 Planarity : 0.002 0.007 450 Dihedral : 14.322 104.588 444 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.29 % Favored : 90.71 % Rotamer: Outliers : 4.44 % Allowed : 10.74 % Favored : 84.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.50 (0.30), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.42 (0.23), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.012 0.003 TYR F 39 PHE 0.012 0.003 PHE A 94 HIS 0.005 0.003 HIS A 50 Details of bonding type rmsd covalent geometry : bond 0.00378 ( 2788) covalent geometry : angle 0.59659 ( 3796) hydrogen bonds : bond 0.03456 ( 28) hydrogen bonds : angle 7.29669 ( 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 40 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 28 time to evaluate : 0.072 Fit side-chains REVERT: A 37 VAL cc_start: 0.6684 (OUTLIER) cc_final: 0.6271 (m) REVERT: A 60 LYS cc_start: 0.6533 (mttt) cc_final: 0.6122 (mtpt) REVERT: D 60 LYS cc_start: 0.6550 (mttt) cc_final: 0.6161 (mtpt) REVERT: D 83 GLU cc_start: 0.8476 (mt-10) cc_final: 0.7913 (tp30) REVERT: E 60 LYS cc_start: 0.7226 (mttt) cc_final: 0.6782 (mtpt) REVERT: E 83 GLU cc_start: 0.8537 (mt-10) cc_final: 0.7891 (tp30) REVERT: B 37 VAL cc_start: 0.6886 (OUTLIER) cc_final: 0.6540 (m) REVERT: B 60 LYS cc_start: 0.6465 (mttt) cc_final: 0.6138 (mtpt) REVERT: C 60 LYS cc_start: 0.6472 (mttt) cc_final: 0.6060 (mtpt) REVERT: F 60 LYS cc_start: 0.7266 (mttt) cc_final: 0.6797 (mtpt) REVERT: F 83 GLU cc_start: 0.8659 (mt-10) cc_final: 0.8018 (tp30) outliers start: 12 outliers final: 10 residues processed: 36 average time/residue: 0.0944 time to fit residues: 3.8658 Evaluate side-chains 40 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 28 time to evaluate : 0.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 79 GLN Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 79 GLN Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain C residue 37 VAL 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: 7.9990 chunk 5 optimal weight: 10.0000 chunk 23 optimal weight: 10.0000 chunk 14 optimal weight: 2.9990 chunk 31 optimal weight: 10.0000 chunk 16 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 chunk 34 optimal weight: 0.7980 chunk 20 optimal weight: 9.9990 chunk 32 optimal weight: 0.7980 chunk 15 optimal weight: 0.7980 overall best weight: 1.6784 ------------------------------------------------------------------------------- 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 = 0.4516 r_free = 0.4516 target = 0.183588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.139849 restraints weight = 2647.024| |-----------------------------------------------------------------------------| r_work (start): 0.3900 rms_B_bonded: 2.39 r_work: 0.3787 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3670 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.2274 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= 0.127 Angle : 0.543 4.586 3796 Z= 0.296 Chirality : 0.050 0.129 498 Planarity : 0.002 0.007 450 Dihedral : 13.672 101.125 444 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 6.67 % Allowed : 8.89 % Favored : 84.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.10 (0.33), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.12 (0.25), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.011 0.003 TYR F 39 PHE 0.010 0.002 PHE B 94 HIS 0.004 0.002 HIS A 50 Details of bonding type rmsd covalent geometry : bond 0.00275 ( 2788) covalent geometry : angle 0.54309 ( 3796) hydrogen bonds : bond 0.02402 ( 28) hydrogen bonds : angle 6.98781 ( 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 43 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 25 time to evaluate : 0.102 Fit side-chains REVERT: A 37 VAL cc_start: 0.6787 (OUTLIER) cc_final: 0.6373 (m) REVERT: A 60 LYS cc_start: 0.6651 (mttt) cc_final: 0.6261 (mtpt) REVERT: D 60 LYS cc_start: 0.6581 (mttt) cc_final: 0.6173 (mtpt) REVERT: D 83 GLU cc_start: 0.8512 (mt-10) cc_final: 0.7954 (tp30) REVERT: E 60 LYS cc_start: 0.7168 (mttt) cc_final: 0.6764 (mtpt) REVERT: E 83 GLU cc_start: 0.8568 (mt-10) cc_final: 0.7949 (tp30) REVERT: B 37 VAL cc_start: 0.6970 (OUTLIER) cc_final: 0.6619 (m) REVERT: B 60 LYS cc_start: 0.6560 (mttt) cc_final: 0.6236 (mtpt) REVERT: C 60 LYS cc_start: 0.6664 (mttt) cc_final: 0.6265 (mtpt) REVERT: F 60 LYS cc_start: 0.7246 (mttt) cc_final: 0.6777 (mtpt) REVERT: F 83 GLU cc_start: 0.8568 (mt-10) cc_final: 0.8038 (tp30) outliers start: 18 outliers final: 15 residues processed: 39 average time/residue: 0.0950 time to fit residues: 4.2674 Evaluate side-chains 42 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 25 time to evaluate : 0.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 79 GLN Chi-restraints excluded: chain 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 C residue 37 VAL Chi-restraints excluded: chain C residue 79 GLN Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain F residue 87 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 8 optimal weight: 6.9990 chunk 16 optimal weight: 5.9990 chunk 17 optimal weight: 7.9990 chunk 15 optimal weight: 0.9990 chunk 10 optimal weight: 5.9990 chunk 22 optimal weight: 8.9990 chunk 21 optimal weight: 7.9990 chunk 32 optimal weight: 4.9990 chunk 14 optimal weight: 0.7980 chunk 2 optimal weight: 6.9990 chunk 12 optimal weight: 0.1980 overall best weight: 2.5986 ------------------------------------------------------------------------------- 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 = 0.4482 r_free = 0.4482 target = 0.179404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.135163 restraints weight = 2623.772| |-----------------------------------------------------------------------------| r_work (start): 0.3859 rms_B_bonded: 2.41 r_work: 0.3742 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3631 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.2534 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= 0.177 Angle : 0.596 4.512 3796 Z= 0.328 Chirality : 0.050 0.128 498 Planarity : 0.002 0.009 450 Dihedral : 13.394 98.253 444 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.84 % Favored : 90.16 % Rotamer: Outliers : 8.89 % Allowed : 7.78 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.95 (0.33), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.01 (0.25), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.012 0.003 TYR B 39 PHE 0.012 0.003 PHE A 94 HIS 0.007 0.004 HIS A 50 Details of bonding type rmsd covalent geometry : bond 0.00388 ( 2788) covalent geometry : angle 0.59598 ( 3796) hydrogen bonds : bond 0.02864 ( 28) hydrogen bonds : angle 7.16389 ( 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 53 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 29 time to evaluate : 0.099 Fit side-chains REVERT: A 37 VAL cc_start: 0.6790 (OUTLIER) cc_final: 0.6379 (m) REVERT: A 60 LYS cc_start: 0.6720 (mttt) cc_final: 0.6310 (mtpt) REVERT: D 60 LYS cc_start: 0.6584 (mttt) cc_final: 0.6185 (mtpt) REVERT: D 83 GLU cc_start: 0.8544 (mt-10) cc_final: 0.7936 (tp30) REVERT: E 60 LYS cc_start: 0.7163 (mttt) cc_final: 0.6785 (mtpt) REVERT: E 83 GLU cc_start: 0.8622 (mt-10) cc_final: 0.8019 (tp30) REVERT: B 37 VAL cc_start: 0.7008 (OUTLIER) cc_final: 0.6642 (m) REVERT: B 60 LYS cc_start: 0.6635 (mttt) cc_final: 0.6302 (mtpt) REVERT: C 60 LYS cc_start: 0.6716 (mttt) cc_final: 0.6360 (mtpt) REVERT: F 60 LYS cc_start: 0.7291 (mttt) cc_final: 0.6838 (mtpt) REVERT: F 83 GLU cc_start: 0.8568 (mt-10) cc_final: 0.8066 (tp30) outliers start: 24 outliers final: 21 residues processed: 47 average time/residue: 0.0877 time to fit residues: 4.8039 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 : 0.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 79 GLN Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 79 GLN Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 79 GLN Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 79 GLN Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 79 GLN Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain F residue 87 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 14 optimal weight: 1.9990 chunk 29 optimal weight: 0.0070 chunk 0 optimal weight: 10.0000 chunk 25 optimal weight: 8.9990 chunk 7 optimal weight: 4.9990 chunk 16 optimal weight: 4.9990 chunk 13 optimal weight: 4.9990 chunk 24 optimal weight: 6.9990 chunk 12 optimal weight: 0.0270 chunk 5 optimal weight: 8.9990 chunk 6 optimal weight: 3.9990 overall best weight: 2.2062 ------------------------------------------------------------------------------- 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 = 0.4514 r_free = 0.4514 target = 0.183280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.138358 restraints weight = 2625.120| |-----------------------------------------------------------------------------| r_work (start): 0.4044 rms_B_bonded: 2.40 r_work: 0.3945 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3834 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.2725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 2788 Z= 0.151 Angle : 0.555 4.460 3796 Z= 0.304 Chirality : 0.049 0.128 498 Planarity : 0.002 0.007 450 Dihedral : 13.148 96.372 444 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.20 % Favored : 91.80 % Rotamer: Outliers : 8.15 % Allowed : 9.26 % Favored : 82.59 % 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 aren not related in a simple way. whole: -3.83 (0.34), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.91 (0.26), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.011 0.003 TYR A 39 PHE 0.012 0.003 PHE A 94 HIS 0.005 0.003 HIS A 50 Details of bonding type rmsd covalent geometry : bond 0.00330 ( 2788) covalent geometry : angle 0.55515 ( 3796) hydrogen bonds : bond 0.02472 ( 28) hydrogen bonds : angle 7.04541 ( 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 48 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 26 time to evaluate : 0.102 Fit side-chains REVERT: A 37 VAL cc_start: 0.6852 (OUTLIER) cc_final: 0.6433 (m) REVERT: A 60 LYS cc_start: 0.6949 (mttt) cc_final: 0.6552 (mtpt) REVERT: D 60 LYS cc_start: 0.6816 (mttt) cc_final: 0.6413 (mtpt) REVERT: E 60 LYS cc_start: 0.7305 (mttt) cc_final: 0.6964 (mtpt) REVERT: E 83 GLU cc_start: 0.8524 (mt-10) cc_final: 0.8072 (tp30) REVERT: B 37 VAL cc_start: 0.7066 (OUTLIER) cc_final: 0.6692 (m) REVERT: B 60 LYS cc_start: 0.6846 (mttt) cc_final: 0.6505 (mtpt) REVERT: C 60 LYS cc_start: 0.6981 (mttt) cc_final: 0.6598 (mtpt) REVERT: F 60 LYS cc_start: 0.7428 (mttt) cc_final: 0.6984 (mtpt) REVERT: F 83 GLU cc_start: 0.8466 (mt-10) cc_final: 0.8081 (tp30) outliers start: 22 outliers final: 19 residues processed: 43 average time/residue: 0.0923 time to fit residues: 4.5632 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 33 optimal weight: 2.9990 chunk 14 optimal weight: 0.8980 chunk 3 optimal weight: 6.9990 chunk 4 optimal weight: 6.9990 chunk 28 optimal weight: 5.9990 chunk 24 optimal weight: 0.0670 chunk 30 optimal weight: 9.9990 chunk 32 optimal weight: 0.3980 chunk 19 optimal weight: 0.8980 chunk 11 optimal weight: 8.9990 chunk 8 optimal weight: 6.9990 overall best weight: 1.0520 ------------------------------------------------------------------------------- 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 = 0.4569 r_free = 0.4569 target = 0.188982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.143649 restraints weight = 2513.339| |-----------------------------------------------------------------------------| r_work (start): 0.3948 rms_B_bonded: 2.35 r_work: 0.3840 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3732 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.2861 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= 0.092 Angle : 0.493 4.242 3796 Z= 0.269 Chirality : 0.049 0.130 498 Planarity : 0.002 0.007 450 Dihedral : 12.679 95.219 444 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.38 % Favored : 92.62 % Rotamer: Outliers : 6.67 % Allowed : 10.74 % Favored : 82.59 % 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 aren not related in a simple way. whole: -3.68 (0.36), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.79 (0.27), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.008 0.002 TYR A 39 PHE 0.009 0.002 PHE B 94 HIS 0.003 0.002 HIS A 50 Details of bonding type rmsd covalent geometry : bond 0.00193 ( 2788) covalent geometry : angle 0.49277 ( 3796) hydrogen bonds : bond 0.02029 ( 28) hydrogen bonds : angle 6.75198 ( 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 43 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 25 time to evaluate : 0.098 Fit side-chains REVERT: A 37 VAL cc_start: 0.6700 (OUTLIER) cc_final: 0.6280 (m) REVERT: A 60 LYS cc_start: 0.6647 (mttt) cc_final: 0.6283 (mtpt) REVERT: D 60 LYS cc_start: 0.6601 (mttt) cc_final: 0.6138 (mtpt) REVERT: E 60 LYS cc_start: 0.7147 (mttt) cc_final: 0.6788 (mtpt) REVERT: B 37 VAL cc_start: 0.6746 (OUTLIER) cc_final: 0.6374 (m) REVERT: B 60 LYS cc_start: 0.6538 (mttt) cc_final: 0.6206 (mtpt) REVERT: C 60 LYS cc_start: 0.6678 (mttt) cc_final: 0.6304 (mtpt) REVERT: F 60 LYS cc_start: 0.7233 (mttt) cc_final: 0.6859 (mtpt) REVERT: F 83 GLU cc_start: 0.8573 (mt-10) cc_final: 0.8062 (tp30) outliers start: 18 outliers final: 13 residues processed: 40 average time/residue: 0.0797 time to fit residues: 3.7188 Evaluate side-chains 40 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 25 time to evaluate : 0.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL 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 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 46 GLU Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain F residue 75 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 19 optimal weight: 4.9990 chunk 22 optimal weight: 8.9990 chunk 9 optimal weight: 2.9990 chunk 27 optimal weight: 6.9990 chunk 17 optimal weight: 10.0000 chunk 26 optimal weight: 0.9980 chunk 35 optimal weight: 4.9990 chunk 10 optimal weight: 0.9990 chunk 11 optimal weight: 7.9990 chunk 3 optimal weight: 0.5980 chunk 29 optimal weight: 2.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- 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 = 0.4614 r_free = 0.4614 target = 0.192502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.143767 restraints weight = 2621.076| |-----------------------------------------------------------------------------| r_work (start): 0.4166 rms_B_bonded: 2.56 r_work: 0.4027 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3919 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.2947 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= 0.124 Angle : 0.525 4.150 3796 Z= 0.287 Chirality : 0.049 0.125 498 Planarity : 0.002 0.007 450 Dihedral : 12.598 93.471 444 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % Rotamer: Outliers : 6.67 % Allowed : 10.74 % Favored : 82.59 % 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 aren not related in a simple way. whole: -3.65 (0.36), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.77 (0.28), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.011 0.002 TYR F 39 PHE 0.011 0.003 PHE B 94 HIS 0.005 0.003 HIS A 50 Details of bonding type rmsd covalent geometry : bond 0.00263 ( 2788) covalent geometry : angle 0.52534 ( 3796) hydrogen bonds : bond 0.02235 ( 28) hydrogen bonds : angle 6.74094 ( 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 43 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 25 time to evaluate : 0.099 Fit side-chains REVERT: A 37 VAL cc_start: 0.6936 (OUTLIER) cc_final: 0.6499 (m) REVERT: A 60 LYS cc_start: 0.7000 (mttt) cc_final: 0.6620 (mtpt) REVERT: D 60 LYS cc_start: 0.6930 (mttt) cc_final: 0.6490 (mtpt) REVERT: E 60 LYS cc_start: 0.7348 (mttt) cc_final: 0.7007 (mtpt) REVERT: B 37 VAL cc_start: 0.6953 (OUTLIER) cc_final: 0.6577 (m) REVERT: B 60 LYS cc_start: 0.6808 (mttt) cc_final: 0.6500 (mtpt) REVERT: C 60 LYS cc_start: 0.6986 (mttt) cc_final: 0.6604 (mtpt) REVERT: F 60 LYS cc_start: 0.7358 (mttt) cc_final: 0.6996 (mtpt) REVERT: F 83 GLU cc_start: 0.8548 (mt-10) cc_final: 0.8093 (tp30) outliers start: 18 outliers final: 16 residues processed: 40 average time/residue: 0.0795 time to fit residues: 3.6922 Evaluate side-chains 43 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 25 time to evaluate : 0.103 ------------------------------------------------------------------------------- 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 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 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: 4.9990 chunk 23 optimal weight: 9.9990 chunk 34 optimal weight: 0.8980 chunk 32 optimal weight: 0.4980 chunk 7 optimal weight: 6.9990 chunk 14 optimal weight: 0.8980 chunk 29 optimal weight: 5.9990 chunk 27 optimal weight: 5.9990 chunk 26 optimal weight: 4.9990 chunk 18 optimal weight: 10.0000 chunk 17 optimal weight: 8.9990 overall best weight: 2.4584 ------------------------------------------------------------------------------- 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 = 0.4575 r_free = 0.4575 target = 0.188419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.140174 restraints weight = 2671.201| |-----------------------------------------------------------------------------| r_work (start): 0.4121 rms_B_bonded: 2.50 r_work: 0.3989 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3877 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.3090 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= 0.165 Angle : 0.574 4.249 3796 Z= 0.315 Chirality : 0.049 0.126 498 Planarity : 0.002 0.008 450 Dihedral : 12.590 91.791 444 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.65 % Favored : 92.35 % Rotamer: Outliers : 6.67 % Allowed : 10.74 % Favored : 82.59 % 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 aren not related in a simple way. whole: -3.69 (0.35), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.81 (0.27), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.013 0.003 TYR B 39 PHE 0.015 0.004 PHE A 94 HIS 0.006 0.003 HIS A 50 Details of bonding type rmsd covalent geometry : bond 0.00366 ( 2788) covalent geometry : angle 0.57380 ( 3796) hydrogen bonds : bond 0.02501 ( 28) hydrogen bonds : angle 6.98391 ( 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 46 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 28 time to evaluate : 0.105 Fit side-chains REVERT: A 37 VAL cc_start: 0.6944 (OUTLIER) cc_final: 0.6493 (m) REVERT: A 60 LYS cc_start: 0.7056 (mttt) cc_final: 0.6657 (mtpt) REVERT: D 60 LYS cc_start: 0.7002 (mttt) cc_final: 0.6571 (mtpt) REVERT: E 60 LYS cc_start: 0.7328 (mttt) cc_final: 0.6986 (mtpt) REVERT: B 37 VAL cc_start: 0.7062 (OUTLIER) cc_final: 0.6682 (m) REVERT: B 60 LYS cc_start: 0.6899 (mttt) cc_final: 0.6587 (mtpt) REVERT: C 60 LYS cc_start: 0.7093 (mttt) cc_final: 0.6733 (mtpt) REVERT: F 60 LYS cc_start: 0.7428 (mttt) cc_final: 0.7005 (mtpt) REVERT: F 83 GLU cc_start: 0.8557 (mt-10) cc_final: 0.8117 (tp30) outliers start: 18 outliers final: 16 residues processed: 41 average time/residue: 0.0923 time to fit residues: 4.3896 Evaluate side-chains 46 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 28 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 D residue 46 GLU Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 79 GLN Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 79 GLN Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 75 THR 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: 0.9980 chunk 2 optimal weight: 3.9990 chunk 25 optimal weight: 5.9990 chunk 11 optimal weight: 6.9990 chunk 6 optimal weight: 10.0000 chunk 15 optimal weight: 5.9990 chunk 20 optimal weight: 2.9990 chunk 31 optimal weight: 0.0870 chunk 18 optimal weight: 9.9990 chunk 35 optimal weight: 0.0270 chunk 33 optimal weight: 10.0000 overall best weight: 1.6220 ------------------------------------------------------------------------------- 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 = 0.4615 r_free = 0.4615 target = 0.193052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.144603 restraints weight = 2617.775| |-----------------------------------------------------------------------------| r_work (start): 0.4167 rms_B_bonded: 2.53 r_work: 0.4024 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3914 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.3162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.015 2788 Z= 0.119 Angle : 0.517 4.183 3796 Z= 0.282 Chirality : 0.049 0.127 498 Planarity : 0.002 0.007 450 Dihedral : 12.324 92.174 444 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 6.67 % Allowed : 10.74 % Favored : 82.59 % 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 aren 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 0.008 0.002 TYR B 39 PHE 0.011 0.003 PHE A 94 HIS 0.005 0.003 HIS A 50 Details of bonding type rmsd covalent geometry : bond 0.00257 ( 2788) covalent geometry : angle 0.51660 ( 3796) hydrogen bonds : bond 0.02123 ( 28) hydrogen bonds : angle 6.75313 ( 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 44 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 26 time to evaluate : 0.097 Fit side-chains REVERT: A 37 VAL cc_start: 0.6942 (OUTLIER) cc_final: 0.6519 (m) REVERT: A 60 LYS cc_start: 0.6974 (mttt) cc_final: 0.6594 (mtpt) REVERT: D 60 LYS cc_start: 0.6932 (mttt) cc_final: 0.6501 (mtpt) REVERT: E 60 LYS cc_start: 0.7352 (mttt) cc_final: 0.7006 (mtpt) REVERT: B 37 VAL cc_start: 0.6955 (OUTLIER) cc_final: 0.6561 (m) REVERT: B 60 LYS cc_start: 0.6862 (mttt) cc_final: 0.6538 (mtpt) REVERT: C 60 LYS cc_start: 0.7083 (mttt) cc_final: 0.6689 (mtpt) REVERT: F 60 LYS cc_start: 0.7354 (mttt) cc_final: 0.6998 (mtpt) REVERT: F 83 GLU cc_start: 0.8546 (mt-10) cc_final: 0.8115 (tp30) outliers start: 18 outliers final: 15 residues processed: 40 average time/residue: 0.0970 time to fit residues: 4.4763 Evaluate side-chains 42 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 25 time to evaluate : 0.095 ------------------------------------------------------------------------------- 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 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 C residue 37 VAL Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 75 THR 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: 0.0980 chunk 25 optimal weight: 4.9990 chunk 22 optimal weight: 0.8980 chunk 30 optimal weight: 8.9990 chunk 17 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 19 optimal weight: 3.9990 chunk 8 optimal weight: 6.9990 chunk 4 optimal weight: 6.9990 chunk 7 optimal weight: 0.4980 chunk 31 optimal weight: 2.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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 = 0.4637 r_free = 0.4637 target = 0.194699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.146086 restraints weight = 2503.450| |-----------------------------------------------------------------------------| r_work (start): 0.4199 rms_B_bonded: 2.50 r_work: 0.4061 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3947 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.3250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 2788 Z= 0.103 Angle : 0.501 4.042 3796 Z= 0.273 Chirality : 0.049 0.128 498 Planarity : 0.002 0.007 450 Dihedral : 12.160 90.974 444 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 6.30 % Allowed : 11.11 % Favored : 82.59 % 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 aren not related in a simple way. whole: -3.58 (0.37), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.72 (0.28), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.008 0.002 TYR A 39 PHE 0.010 0.002 PHE A 94 HIS 0.004 0.002 HIS A 50 Details of bonding type rmsd covalent geometry : bond 0.00219 ( 2788) covalent geometry : angle 0.50141 ( 3796) hydrogen bonds : bond 0.01992 ( 28) hydrogen bonds : angle 6.56756 ( 84) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 997.44 seconds wall clock time: 17 minutes 48.41 seconds (1068.41 seconds total)