Starting phenix.real_space_refine on Tue Mar 3 11:05:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xjx_33236/03_2026/7xjx_33236.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xjx_33236/03_2026/7xjx_33236.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7xjx_33236/03_2026/7xjx_33236.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xjx_33236/03_2026/7xjx_33236.map" model { file = "/net/cci-nas-00/data/ceres_data/7xjx_33236/03_2026/7xjx_33236.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xjx_33236/03_2026/7xjx_33236.cif" } resolution = 2.7 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= 0.005 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 1644 2.51 5 N 456 2.21 5 O 528 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 2628 Number of models: 1 Model: "" Number of chains: 1 Chain: "B" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 438 Classifications: {'peptide': 63} Link IDs: {'TRANS': 62} Restraints were copied for chains: A, E, C, F, D Time building chain proxies: 0.45, per 1000 atoms: 0.17 Number of scatterers: 2628 At special positions: 0 Unit cell: (108.272, 95.408, 31.088, 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 528 8.00 N 456 7.00 C 1644 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: 0.17 Conformation dependent library (CDL) restraints added in 108.3 milliseconds 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 648 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 6 sheets defined 0.0% alpha, 34.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.04 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'E' and resid 46 through 56 removed outlier: 7.570A pdb=" N GLY B 47 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 10.111A pdb=" N HIS E 50 " --> pdb=" O GLY B 47 " (cutoff:3.500A) removed outlier: 8.911A pdb=" N VAL B 49 " --> pdb=" O HIS E 50 " (cutoff:3.500A) removed outlier: 9.185A pdb=" N VAL E 52 " --> pdb=" O VAL B 49 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N GLY B 51 " --> pdb=" O VAL E 52 " (cutoff:3.500A) removed outlier: 8.102A pdb=" N THR E 54 " --> pdb=" O GLY B 51 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N ALA B 53 " --> pdb=" O THR E 54 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N ALA E 56 " --> pdb=" O ALA B 53 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N VAL B 55 " --> pdb=" O ALA E 56 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N VAL B 48 " --> pdb=" O GLY F 47 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N VAL F 49 " --> pdb=" O VAL B 48 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N HIS B 50 " --> pdb=" O VAL F 49 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N GLY F 51 " --> pdb=" O HIS B 50 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 60 through 65 removed outlier: 6.476A pdb=" N GLU B 61 " --> pdb=" O GLN F 62 " (cutoff:3.500A) removed outlier: 8.061A pdb=" N THR F 64 " --> pdb=" O GLU B 61 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N VAL B 63 " --> pdb=" O THR F 64 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 71 through 78 removed outlier: 6.417A pdb=" N THR B 72 " --> pdb=" O GLY E 73 " (cutoff:3.500A) removed outlier: 8.698A pdb=" N THR E 75 " --> pdb=" O THR B 72 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N VAL B 74 " --> pdb=" O THR E 75 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N VAL E 77 " --> pdb=" O VAL B 74 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N ALA B 76 " --> pdb=" O VAL E 77 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N THR F 72 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N GLY B 73 " --> pdb=" O THR F 72 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N VAL B 77 " --> pdb=" O ALA F 76 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N ALA F 78 " --> pdb=" O VAL B 77 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 46 through 56 removed outlier: 7.551A pdb=" N GLY A 47 " --> pdb=" O VAL C 48 " (cutoff:3.500A) removed outlier: 10.091A pdb=" N HIS C 50 " --> pdb=" O GLY A 47 " (cutoff:3.500A) removed outlier: 8.893A pdb=" N VAL A 49 " --> pdb=" O HIS C 50 " (cutoff:3.500A) removed outlier: 9.169A pdb=" N VAL C 52 " --> pdb=" O VAL A 49 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N GLY A 51 " --> pdb=" O VAL C 52 " (cutoff:3.500A) removed outlier: 8.091A pdb=" N THR C 54 " --> pdb=" O GLY A 51 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ALA A 53 " --> pdb=" O THR C 54 " (cutoff:3.500A) removed outlier: 7.981A pdb=" N ALA C 56 " --> pdb=" O ALA A 53 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N VAL A 55 " --> pdb=" O ALA C 56 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N VAL A 48 " --> pdb=" O GLY D 47 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N VAL D 49 " --> pdb=" O VAL A 48 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N HIS A 50 " --> pdb=" O VAL D 49 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N GLY D 51 " --> pdb=" O HIS A 50 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 60 through 65 removed outlier: 6.490A pdb=" N GLU A 61 " --> pdb=" O GLN D 62 " (cutoff:3.500A) removed outlier: 8.073A pdb=" N THR D 64 " --> pdb=" O GLU A 61 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N VAL A 63 " --> pdb=" O THR D 64 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 71 through 78 removed outlier: 6.408A pdb=" N THR A 72 " --> pdb=" O GLY C 73 " (cutoff:3.500A) removed outlier: 8.697A pdb=" N THR C 75 " --> pdb=" O THR A 72 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N VAL A 74 " --> pdb=" O THR C 75 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N VAL C 77 " --> pdb=" O VAL A 74 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N ALA A 76 " --> pdb=" O VAL C 77 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N THR D 72 " --> pdb=" O VAL A 71 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N GLY A 73 " --> pdb=" O THR D 72 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N VAL A 77 " --> pdb=" O ALA D 76 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N ALA D 78 " --> pdb=" O VAL A 77 " (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 0 stacking parallelities Total time for adding SS restraints: 0.20 Time building geometry restraints manager: 0.24 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: 462 1.28 - 1.35: 408 1.35 - 1.41: 99 1.41 - 1.48: 441 1.48 - 1.54: 1230 Bond restraints: 2640 Sorted by residual: bond pdb=" CA GLY A 68 " pdb=" C GLY A 68 " ideal model delta sigma weight residual 1.530 1.515 0.016 1.04e-02 9.25e+03 2.25e+00 bond pdb=" CA GLY C 68 " pdb=" C GLY C 68 " ideal model delta sigma weight residual 1.530 1.515 0.016 1.04e-02 9.25e+03 2.24e+00 bond pdb=" CA GLY B 68 " pdb=" C GLY B 68 " ideal model delta sigma weight residual 1.530 1.515 0.016 1.04e-02 9.25e+03 2.23e+00 bond pdb=" CA GLY D 68 " pdb=" C GLY D 68 " ideal model delta sigma weight residual 1.530 1.515 0.015 1.04e-02 9.25e+03 2.19e+00 bond pdb=" CA GLY E 68 " pdb=" C GLY E 68 " ideal model delta sigma weight residual 1.530 1.515 0.015 1.04e-02 9.25e+03 2.14e+00 ... (remaining 2635 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.08: 3134 1.08 - 2.15: 354 2.15 - 3.23: 55 3.23 - 4.30: 15 4.30 - 5.38: 12 Bond angle restraints: 3570 Sorted by residual: angle pdb=" N HIS E 50 " pdb=" CA HIS E 50 " pdb=" C HIS E 50 " ideal model delta sigma weight residual 108.99 113.74 -4.75 1.57e+00 4.06e-01 9.16e+00 angle pdb=" N HIS B 50 " pdb=" CA HIS B 50 " pdb=" C HIS B 50 " ideal model delta sigma weight residual 108.99 113.74 -4.75 1.57e+00 4.06e-01 9.16e+00 angle pdb=" N HIS C 50 " pdb=" CA HIS C 50 " pdb=" C HIS C 50 " ideal model delta sigma weight residual 108.99 113.74 -4.75 1.57e+00 4.06e-01 9.15e+00 angle pdb=" N HIS F 50 " pdb=" CA HIS F 50 " pdb=" C HIS F 50 " ideal model delta sigma weight residual 108.99 113.69 -4.70 1.57e+00 4.06e-01 8.98e+00 angle pdb=" N HIS A 50 " pdb=" CA HIS A 50 " pdb=" C HIS A 50 " ideal model delta sigma weight residual 108.99 113.69 -4.70 1.57e+00 4.06e-01 8.95e+00 ... (remaining 3565 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 9.68: 1206 9.68 - 19.36: 240 19.36 - 29.03: 60 29.03 - 38.71: 24 38.71 - 48.39: 18 Dihedral angle restraints: 1548 sinusoidal: 522 harmonic: 1026 Sorted by residual: dihedral pdb=" CA ALA C 89 " pdb=" C ALA C 89 " pdb=" N ALA C 90 " pdb=" CA ALA C 90 " ideal model delta harmonic sigma weight residual -180.00 -157.80 -22.20 0 5.00e+00 4.00e-02 1.97e+01 dihedral pdb=" CA ALA E 89 " pdb=" C ALA E 89 " pdb=" N ALA E 90 " pdb=" CA ALA E 90 " ideal model delta harmonic sigma weight residual -180.00 -157.84 -22.16 0 5.00e+00 4.00e-02 1.96e+01 dihedral pdb=" CA ALA A 89 " pdb=" C ALA A 89 " pdb=" N ALA A 90 " pdb=" CA ALA A 90 " ideal model delta harmonic sigma weight residual 180.00 -157.85 -22.15 0 5.00e+00 4.00e-02 1.96e+01 ... (remaining 1545 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 243 0.036 - 0.071: 116 0.071 - 0.106: 61 0.106 - 0.141: 30 0.141 - 0.177: 18 Chirality restraints: 468 Sorted by residual: 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 2.62 -0.18 2.00e-01 2.50e+01 7.80e-01 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 2.62 -0.18 2.00e-01 2.50e+01 7.74e-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 2.62 -0.17 2.00e-01 2.50e+01 7.65e-01 ... (remaining 465 not shown) Planarity restraints: 444 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL E 48 " 0.008 2.00e-02 2.50e+03 1.66e-02 2.75e+00 pdb=" C VAL E 48 " -0.029 2.00e-02 2.50e+03 pdb=" O VAL E 48 " 0.011 2.00e-02 2.50e+03 pdb=" N VAL E 49 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL D 48 " -0.008 2.00e-02 2.50e+03 1.66e-02 2.74e+00 pdb=" C VAL D 48 " 0.029 2.00e-02 2.50e+03 pdb=" O VAL D 48 " -0.011 2.00e-02 2.50e+03 pdb=" N VAL D 49 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL F 48 " 0.008 2.00e-02 2.50e+03 1.65e-02 2.71e+00 pdb=" C VAL F 48 " -0.028 2.00e-02 2.50e+03 pdb=" O VAL F 48 " 0.011 2.00e-02 2.50e+03 pdb=" N VAL F 49 " 0.010 2.00e-02 2.50e+03 ... (remaining 441 not shown) Histogram of nonbonded interaction distances: 2.44 - 2.93: 1203 2.93 - 3.42: 2369 3.42 - 3.92: 3923 3.92 - 4.41: 4245 4.41 - 4.90: 9221 Nonbonded interactions: 20961 Sorted by model distance: nonbonded pdb=" O THR C 64 " pdb=" OG1 THR C 64 " model vdw 2.438 3.040 nonbonded pdb=" O THR B 64 " pdb=" OG1 THR B 64 " model vdw 2.438 3.040 nonbonded pdb=" O THR D 64 " pdb=" OG1 THR D 64 " model vdw 2.439 3.040 nonbonded pdb=" O THR A 64 " pdb=" OG1 THR A 64 " model vdw 2.439 3.040 nonbonded pdb=" O THR E 64 " pdb=" OG1 THR E 64 " model vdw 2.439 3.040 ... (remaining 20956 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 'B' selection = chain 'A' selection = chain 'E' selection = chain 'C' selection = chain 'F' selection = chain 'D' } 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: 1.320 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: 0.030 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 3.800 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: 0.010 Load rotamer database and sin/cos tables:5.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 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 0.033 2640 Z= 0.388 Angle : 0.806 5.379 3570 Z= 0.484 Chirality : 0.063 0.177 468 Planarity : 0.003 0.017 444 Dihedral : 12.769 48.390 900 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 13.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.39 % Favored : 83.61 % Rotamer: Outliers : 0.00 % Allowed : 15.56 % Favored : 84.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.02 (0.31), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.82 (0.24), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.009 0.002 TYR F 39 PHE 0.002 0.001 PHE C 94 HIS 0.003 0.002 HIS E 50 Details of bonding type rmsd covalent geometry : bond 0.00794 ( 2640) covalent geometry : angle 0.80574 ( 3570) hydrogen bonds : bond 0.16493 ( 28) hydrogen bonds : angle 7.48459 ( 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 43 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.110 Fit side-chains REVERT: B 54 THR cc_start: 0.8956 (p) cc_final: 0.8731 (p) REVERT: D 60 LYS cc_start: 0.8053 (ttmt) cc_final: 0.7814 (tttt) outliers start: 0 outliers final: 0 residues processed: 43 average time/residue: 0.5092 time to fit residues: 22.4058 Evaluate side-chains 39 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 39 time to evaluate : 0.106 ------------------------------------------------------------------------------- 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: 0.0270 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 6.9990 chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 30 optimal weight: 9.9990 chunk 22 optimal weight: 4.9990 chunk 13 optimal weight: 0.9990 overall best weight: 1.2044 ------------------------------------------------------------------------------- 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 = 0.4556 r_free = 0.4556 target = 0.193198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.160199 restraints weight = 3218.765| |-----------------------------------------------------------------------------| r_work (start): 0.4208 rms_B_bonded: 2.43 r_work: 0.4132 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.4025 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.4025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.1306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 2640 Z= 0.118 Angle : 0.515 3.461 3570 Z= 0.297 Chirality : 0.051 0.127 468 Planarity : 0.002 0.011 444 Dihedral : 5.803 17.421 378 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.20 % Favored : 88.80 % Rotamer: Outliers : 4.07 % Allowed : 23.33 % Favored : 72.59 % 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: -4.45 (0.33), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.38 (0.25), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.005 0.001 TYR C 39 PHE 0.002 0.000 PHE B 94 HIS 0.005 0.003 HIS C 50 Details of bonding type rmsd covalent geometry : bond 0.00241 ( 2640) covalent geometry : angle 0.51511 ( 3570) hydrogen bonds : bond 0.02605 ( 28) hydrogen bonds : angle 5.44255 ( 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 50 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 39 time to evaluate : 0.181 Fit side-chains REVERT: B 43 LYS cc_start: 0.8191 (OUTLIER) cc_final: 0.7509 (mptt) REVERT: B 60 LYS cc_start: 0.7986 (ttpt) cc_final: 0.7746 (tppp) REVERT: E 83 GLU cc_start: 0.7693 (tm-30) cc_final: 0.7196 (tm-30) REVERT: C 60 LYS cc_start: 0.8286 (tttt) cc_final: 0.8036 (tttt) REVERT: F 43 LYS cc_start: 0.8032 (OUTLIER) cc_final: 0.7771 (ptpp) REVERT: D 43 LYS cc_start: 0.8262 (OUTLIER) cc_final: 0.8014 (mptt) outliers start: 11 outliers final: 5 residues processed: 42 average time/residue: 0.5405 time to fit residues: 23.2199 Evaluate side-chains 42 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 34 time to evaluate : 0.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 LYS Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain C residue 43 LYS Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain F residue 43 LYS Chi-restraints excluded: chain D residue 43 LYS Chi-restraints excluded: chain D residue 75 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 8 optimal weight: 8.9990 chunk 22 optimal weight: 0.0000 chunk 6 optimal weight: 10.0000 chunk 35 optimal weight: 0.0970 chunk 26 optimal weight: 6.9990 chunk 4 optimal weight: 4.9990 chunk 16 optimal weight: 0.7980 chunk 33 optimal weight: 3.9990 chunk 31 optimal weight: 5.9990 chunk 2 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 overall best weight: 0.7786 ------------------------------------------------------------------------------- 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 = 0.4596 r_free = 0.4596 target = 0.196874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.164714 restraints weight = 3246.204| |-----------------------------------------------------------------------------| r_work (start): 0.4259 rms_B_bonded: 2.41 r_work: 0.4186 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.4081 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.4081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.1741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.011 2640 Z= 0.086 Angle : 0.455 3.175 3570 Z= 0.264 Chirality : 0.050 0.123 468 Planarity : 0.002 0.009 444 Dihedral : 5.097 16.071 378 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.74 % Favored : 91.26 % Rotamer: Outliers : 5.93 % Allowed : 21.48 % Favored : 72.59 % 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: -3.88 (0.35), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.95 (0.27), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.005 0.001 TYR C 39 PHE 0.001 0.000 PHE C 94 HIS 0.004 0.003 HIS B 50 Details of bonding type rmsd covalent geometry : bond 0.00175 ( 2640) covalent geometry : angle 0.45454 ( 3570) hydrogen bonds : bond 0.02030 ( 28) hydrogen bonds : angle 5.17159 ( 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 54 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 38 time to evaluate : 0.097 Fit side-chains REVERT: B 43 LYS cc_start: 0.8279 (OUTLIER) cc_final: 0.8024 (ptpp) REVERT: B 60 LYS cc_start: 0.7955 (ttpt) cc_final: 0.7698 (tppp) REVERT: E 83 GLU cc_start: 0.7698 (tm-30) cc_final: 0.7250 (tm-30) REVERT: C 43 LYS cc_start: 0.8183 (OUTLIER) cc_final: 0.7791 (mptt) REVERT: C 60 LYS cc_start: 0.8305 (tttt) cc_final: 0.8050 (tttt) REVERT: D 60 LYS cc_start: 0.8141 (tttt) cc_final: 0.7726 (tmmm) outliers start: 16 outliers final: 7 residues processed: 46 average time/residue: 0.5067 time to fit residues: 23.8551 Evaluate side-chains 47 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 38 time to evaluate : 0.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 43 LYS Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain C residue 43 LYS Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 75 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 3 optimal weight: 5.9990 chunk 15 optimal weight: 1.9990 chunk 17 optimal weight: 6.9990 chunk 12 optimal weight: 10.0000 chunk 21 optimal weight: 6.9990 chunk 6 optimal weight: 10.0000 chunk 31 optimal weight: 6.9990 chunk 23 optimal weight: 0.9980 chunk 18 optimal weight: 6.9990 chunk 16 optimal weight: 4.9990 chunk 22 optimal weight: 0.7980 overall best weight: 2.9586 ------------------------------------------------------------------------------- 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 = 0.4505 r_free = 0.4505 target = 0.188396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.154579 restraints weight = 3192.457| |-----------------------------------------------------------------------------| r_work (start): 0.4155 rms_B_bonded: 2.42 r_work: 0.4073 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3967 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.1599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.022 2640 Z= 0.220 Angle : 0.570 3.651 3570 Z= 0.322 Chirality : 0.052 0.125 468 Planarity : 0.002 0.009 444 Dihedral : 6.198 19.337 378 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.48 % Favored : 88.52 % Rotamer: Outliers : 7.41 % Allowed : 17.41 % Favored : 75.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.80 (0.36), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.89 (0.28), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.010 0.002 TYR C 39 PHE 0.004 0.001 PHE C 94 HIS 0.007 0.004 HIS B 50 Details of bonding type rmsd covalent geometry : bond 0.00494 ( 2640) covalent geometry : angle 0.56989 ( 3570) hydrogen bonds : bond 0.02310 ( 28) hydrogen bonds : angle 5.24331 ( 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 57 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 37 time to evaluate : 0.099 Fit side-chains REVERT: B 43 LYS cc_start: 0.8224 (OUTLIER) cc_final: 0.7688 (mptt) REVERT: B 60 LYS cc_start: 0.8013 (ttpt) cc_final: 0.7766 (tppp) REVERT: E 83 GLU cc_start: 0.7754 (tm-30) cc_final: 0.7315 (tm-30) REVERT: C 60 LYS cc_start: 0.8384 (tttt) cc_final: 0.8149 (tttt) REVERT: F 60 LYS cc_start: 0.8083 (tttt) cc_final: 0.7849 (tmmm) REVERT: D 60 LYS cc_start: 0.8203 (tttt) cc_final: 0.7729 (tmmm) outliers start: 20 outliers final: 14 residues processed: 50 average time/residue: 0.4493 time to fit residues: 23.1206 Evaluate side-chains 51 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 36 time to evaluate : 0.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 43 LYS Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 43 LYS Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 75 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 25 optimal weight: 6.9990 chunk 19 optimal weight: 3.9990 chunk 34 optimal weight: 4.9990 chunk 11 optimal weight: 9.9990 chunk 14 optimal weight: 6.9990 chunk 1 optimal weight: 0.9990 chunk 30 optimal weight: 10.0000 chunk 7 optimal weight: 4.9990 chunk 13 optimal weight: 7.9990 chunk 28 optimal weight: 1.9990 chunk 18 optimal weight: 7.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4489 r_free = 0.4489 target = 0.187020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.153508 restraints weight = 3203.915| |-----------------------------------------------------------------------------| r_work (start): 0.4135 rms_B_bonded: 2.41 r_work: 0.4053 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3947 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.1661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.025 2640 Z= 0.248 Angle : 0.603 3.837 3570 Z= 0.341 Chirality : 0.053 0.124 468 Planarity : 0.003 0.013 444 Dihedral : 6.554 20.854 378 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.75 % Favored : 88.25 % Rotamer: Outliers : 7.04 % Allowed : 18.52 % Favored : 74.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.79 (0.36), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.88 (0.28), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.009 0.002 TYR C 39 PHE 0.005 0.001 PHE C 94 HIS 0.007 0.004 HIS B 50 Details of bonding type rmsd covalent geometry : bond 0.00555 ( 2640) covalent geometry : angle 0.60301 ( 3570) hydrogen bonds : bond 0.02410 ( 28) hydrogen bonds : angle 5.33478 ( 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 54 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 35 time to evaluate : 0.101 Fit side-chains REVERT: B 43 LYS cc_start: 0.8283 (OUTLIER) cc_final: 0.7747 (mptt) REVERT: B 60 LYS cc_start: 0.8014 (OUTLIER) cc_final: 0.7745 (tppp) REVERT: E 83 GLU cc_start: 0.7684 (tm-30) cc_final: 0.7139 (tm-30) REVERT: C 60 LYS cc_start: 0.8386 (ttmt) cc_final: 0.8012 (ttpt) REVERT: F 60 LYS cc_start: 0.8117 (tttt) cc_final: 0.7836 (tmmm) REVERT: D 60 LYS cc_start: 0.8207 (tttt) cc_final: 0.7912 (tttp) outliers start: 19 outliers final: 15 residues processed: 45 average time/residue: 0.4561 time to fit residues: 21.0759 Evaluate side-chains 52 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 35 time to evaluate : 0.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 43 LYS Chi-restraints excluded: chain B residue 60 LYS Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 43 LYS Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain D residue 75 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 35 optimal weight: 0.4980 chunk 30 optimal weight: 9.9990 chunk 2 optimal weight: 1.9990 chunk 1 optimal weight: 0.6980 chunk 6 optimal weight: 9.9990 chunk 14 optimal weight: 1.9990 chunk 4 optimal weight: 6.9990 chunk 34 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 9 optimal weight: 2.9990 chunk 27 optimal weight: 4.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 62 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4549 r_free = 0.4549 target = 0.193015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.161064 restraints weight = 3204.402| |-----------------------------------------------------------------------------| r_work (start): 0.4214 rms_B_bonded: 2.36 r_work: 0.4138 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.4035 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.4035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.1977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 2640 Z= 0.110 Angle : 0.500 5.667 3570 Z= 0.285 Chirality : 0.049 0.125 468 Planarity : 0.002 0.011 444 Dihedral : 5.683 20.587 378 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.11 % Favored : 89.89 % Rotamer: Outliers : 5.19 % Allowed : 20.74 % Favored : 74.07 % 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: -3.59 (0.38), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.73 (0.29), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.005 0.001 TYR C 39 PHE 0.002 0.000 PHE C 94 HIS 0.005 0.003 HIS B 50 Details of bonding type rmsd covalent geometry : bond 0.00231 ( 2640) covalent geometry : angle 0.50041 ( 3570) hydrogen bonds : bond 0.01834 ( 28) hydrogen bonds : angle 5.21052 ( 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: 14 poor density : 34 time to evaluate : 0.100 Fit side-chains REVERT: B 43 LYS cc_start: 0.8275 (OUTLIER) cc_final: 0.7846 (mptt) REVERT: B 60 LYS cc_start: 0.7909 (ttpt) cc_final: 0.7648 (tppp) REVERT: E 83 GLU cc_start: 0.7639 (tm-30) cc_final: 0.7171 (tm-30) REVERT: D 60 LYS cc_start: 0.8162 (tttt) cc_final: 0.7731 (tmmm) outliers start: 14 outliers final: 10 residues processed: 43 average time/residue: 0.5176 time to fit residues: 22.8529 Evaluate side-chains 42 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 31 time to evaluate : 0.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 43 LYS Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 75 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 2 optimal weight: 2.9990 chunk 9 optimal weight: 8.9990 chunk 8 optimal weight: 3.9990 chunk 12 optimal weight: 5.9990 chunk 24 optimal weight: 10.0000 chunk 1 optimal weight: 1.9990 chunk 29 optimal weight: 6.9990 chunk 5 optimal weight: 5.9990 chunk 27 optimal weight: 0.0570 chunk 7 optimal weight: 1.9990 chunk 35 optimal weight: 8.9990 overall best weight: 2.2106 ------------------------------------------------------------------------------- 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 = 0.4511 r_free = 0.4511 target = 0.189498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.156503 restraints weight = 3178.267| |-----------------------------------------------------------------------------| r_work (start): 0.4170 rms_B_bonded: 2.38 r_work: 0.4093 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3991 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.1957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 2640 Z= 0.173 Angle : 0.585 7.820 3570 Z= 0.325 Chirality : 0.050 0.125 468 Planarity : 0.002 0.009 444 Dihedral : 6.045 19.858 378 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.48 % Favored : 88.52 % Rotamer: Outliers : 5.19 % Allowed : 21.85 % Favored : 72.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.54 (0.38), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.69 (0.29), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.008 0.002 TYR C 39 PHE 0.004 0.001 PHE C 94 HIS 0.006 0.003 HIS B 50 Details of bonding type rmsd covalent geometry : bond 0.00389 ( 2640) covalent geometry : angle 0.58505 ( 3570) hydrogen bonds : bond 0.02089 ( 28) hydrogen bonds : angle 5.19079 ( 84) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 36 time to evaluate : 0.105 Fit side-chains REVERT: B 43 LYS cc_start: 0.8291 (OUTLIER) cc_final: 0.7742 (mptt) REVERT: B 60 LYS cc_start: 0.7916 (ttpt) cc_final: 0.7676 (tppp) REVERT: A 60 LYS cc_start: 0.7940 (tttt) cc_final: 0.7692 (tmtm) REVERT: E 83 GLU cc_start: 0.7704 (tm-30) cc_final: 0.7232 (tm-30) REVERT: D 60 LYS cc_start: 0.8144 (tttt) cc_final: 0.7876 (tttp) outliers start: 14 outliers final: 10 residues processed: 45 average time/residue: 0.5491 time to fit residues: 25.3291 Evaluate side-chains 46 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 35 time to evaluate : 0.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 43 LYS Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 75 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 12 optimal weight: 0.5980 chunk 30 optimal weight: 9.9990 chunk 22 optimal weight: 0.6980 chunk 31 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 11 optimal weight: 6.9990 chunk 35 optimal weight: 4.9990 chunk 6 optimal weight: 9.9990 chunk 34 optimal weight: 2.9990 chunk 4 optimal weight: 10.0000 chunk 16 optimal weight: 0.7980 overall best weight: 1.2182 ------------------------------------------------------------------------------- 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 = 0.4552 r_free = 0.4552 target = 0.193272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.161086 restraints weight = 3284.253| |-----------------------------------------------------------------------------| r_work (start): 0.4215 rms_B_bonded: 2.40 r_work: 0.4138 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.4035 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.4035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.2175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 2640 Z= 0.113 Angle : 0.529 6.947 3570 Z= 0.296 Chirality : 0.049 0.126 468 Planarity : 0.002 0.008 444 Dihedral : 5.600 20.860 378 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.38 % Favored : 89.62 % Rotamer: Outliers : 4.07 % Allowed : 22.96 % Favored : 72.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.43 (0.39), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.60 (0.30), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.005 0.001 TYR C 39 PHE 0.001 0.000 PHE C 94 HIS 0.005 0.003 HIS B 50 Details of bonding type rmsd covalent geometry : bond 0.00243 ( 2640) covalent geometry : angle 0.52898 ( 3570) hydrogen bonds : bond 0.01815 ( 28) hydrogen bonds : angle 5.14727 ( 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 49 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 38 time to evaluate : 0.110 Fit side-chains REVERT: B 43 LYS cc_start: 0.8267 (OUTLIER) cc_final: 0.7894 (mptt) REVERT: B 60 LYS cc_start: 0.7938 (ttpt) cc_final: 0.7726 (tppp) REVERT: A 60 LYS cc_start: 0.7899 (tttt) cc_final: 0.7655 (tmtm) REVERT: E 83 GLU cc_start: 0.7707 (tm-30) cc_final: 0.7265 (tm-30) REVERT: D 60 LYS cc_start: 0.8123 (tttt) cc_final: 0.7749 (tmmm) outliers start: 11 outliers final: 9 residues processed: 46 average time/residue: 0.5270 time to fit residues: 24.8807 Evaluate side-chains 44 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 34 time to evaluate : 0.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 43 LYS Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 75 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 12 optimal weight: 5.9990 chunk 15 optimal weight: 0.0570 chunk 16 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 17 optimal weight: 0.5980 chunk 27 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 8 optimal weight: 4.9990 chunk 11 optimal weight: 9.9990 chunk 20 optimal weight: 0.9990 chunk 25 optimal weight: 7.9990 overall best weight: 1.1304 ------------------------------------------------------------------------------- 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 = 0.4571 r_free = 0.4571 target = 0.194403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.161327 restraints weight = 3250.173| |-----------------------------------------------------------------------------| r_work (start): 0.4223 rms_B_bonded: 2.44 r_work: 0.4146 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.4042 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.4042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.2286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 2640 Z= 0.109 Angle : 0.519 7.696 3570 Z= 0.292 Chirality : 0.049 0.127 468 Planarity : 0.002 0.008 444 Dihedral : 5.456 20.422 378 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.29 % Favored : 90.71 % Rotamer: Outliers : 4.07 % Allowed : 22.96 % Favored : 72.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.30 (0.40), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.51 (0.30), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.004 0.001 TYR C 39 PHE 0.002 0.000 PHE C 94 HIS 0.005 0.003 HIS B 50 Details of bonding type rmsd covalent geometry : bond 0.00237 ( 2640) covalent geometry : angle 0.51885 ( 3570) hydrogen bonds : bond 0.01781 ( 28) hydrogen bonds : angle 5.03510 ( 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 48 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 37 time to evaluate : 0.071 Fit side-chains REVERT: B 43 LYS cc_start: 0.8352 (OUTLIER) cc_final: 0.8146 (ptpp) REVERT: A 60 LYS cc_start: 0.7892 (tttt) cc_final: 0.7676 (tmtm) REVERT: E 83 GLU cc_start: 0.7761 (tm-30) cc_final: 0.7340 (tm-30) REVERT: C 83 GLU cc_start: 0.7725 (tm-30) cc_final: 0.7425 (tm-30) REVERT: D 60 LYS cc_start: 0.8096 (tttt) cc_final: 0.7742 (tmmm) outliers start: 11 outliers final: 10 residues processed: 45 average time/residue: 0.4837 time to fit residues: 22.4042 Evaluate side-chains 47 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 36 time to evaluate : 0.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 43 LYS Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 75 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 16 optimal weight: 0.9980 chunk 13 optimal weight: 0.0870 chunk 18 optimal weight: 0.3980 chunk 10 optimal weight: 9.9990 chunk 7 optimal weight: 1.9990 chunk 3 optimal weight: 8.9990 chunk 2 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 chunk 4 optimal weight: 0.8980 chunk 33 optimal weight: 3.9990 chunk 15 optimal weight: 0.5980 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 62 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4636 r_free = 0.4636 target = 0.200430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4324 r_free = 0.4324 target = 0.167933 restraints weight = 3246.247| |-----------------------------------------------------------------------------| r_work (start): 0.4299 rms_B_bonded: 2.45 r_work: 0.4224 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.4121 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.4121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.2642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 2640 Z= 0.084 Angle : 0.512 7.767 3570 Z= 0.284 Chirality : 0.049 0.133 468 Planarity : 0.001 0.007 444 Dihedral : 4.957 17.935 378 Min Nonbonded Distance : 2.638 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.02 % Favored : 90.98 % Rotamer: Outliers : 3.70 % Allowed : 23.70 % Favored : 72.59 % 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: -3.19 (0.41), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.42 (0.31), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.003 0.000 TYR C 39 PHE 0.001 0.000 PHE C 94 HIS 0.005 0.002 HIS E 50 Details of bonding type rmsd covalent geometry : bond 0.00176 ( 2640) covalent geometry : angle 0.51221 ( 3570) hydrogen bonds : bond 0.01654 ( 28) hydrogen bonds : angle 4.94559 ( 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 48 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 38 time to evaluate : 0.115 Fit side-chains REVERT: B 83 GLU cc_start: 0.7276 (tm-30) cc_final: 0.7049 (tm-30) REVERT: A 60 LYS cc_start: 0.7824 (tttt) cc_final: 0.7512 (tmtm) REVERT: E 83 GLU cc_start: 0.7702 (tm-30) cc_final: 0.7323 (tm-30) REVERT: D 60 LYS cc_start: 0.8075 (tttt) cc_final: 0.7726 (tmmm) outliers start: 10 outliers final: 8 residues processed: 45 average time/residue: 0.5263 time to fit residues: 24.2866 Evaluate side-chains 45 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 37 time to evaluate : 0.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 75 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 32 optimal weight: 7.9990 chunk 17 optimal weight: 9.9990 chunk 14 optimal weight: 6.9990 chunk 13 optimal weight: 0.2980 chunk 25 optimal weight: 4.9990 chunk 0 optimal weight: 9.9990 chunk 35 optimal weight: 10.0000 chunk 22 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 23 optimal weight: 8.9990 overall best weight: 2.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 62 GLN C 62 GLN F 62 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4514 r_free = 0.4514 target = 0.189500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.155919 restraints weight = 3236.109| |-----------------------------------------------------------------------------| r_work (start): 0.4155 rms_B_bonded: 2.44 r_work: 0.4076 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3971 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.2295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 2640 Z= 0.198 Angle : 0.635 6.884 3570 Z= 0.345 Chirality : 0.050 0.126 468 Planarity : 0.002 0.018 444 Dihedral : 6.008 19.853 378 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.66 % Favored : 89.34 % Rotamer: Outliers : 3.70 % Allowed : 22.96 % Favored : 73.33 % 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 are not related in a simple way. whole: -3.33 (0.40), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.53 (0.30), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.008 0.002 TYR C 39 PHE 0.004 0.001 PHE C 94 HIS 0.007 0.004 HIS B 50 Details of bonding type rmsd covalent geometry : bond 0.00459 ( 2640) covalent geometry : angle 0.63525 ( 3570) hydrogen bonds : bond 0.01923 ( 28) hydrogen bonds : angle 5.00968 ( 84) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1311.89 seconds wall clock time: 23 minutes 2.03 seconds (1382.03 seconds total)