Starting phenix.real_space_refine on Tue Mar 3 11:06:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9wao_65825/03_2026/9wao_65825.cif Found real_map, /net/cci-nas-00/data/ceres_data/9wao_65825/03_2026/9wao_65825.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9wao_65825/03_2026/9wao_65825.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9wao_65825/03_2026/9wao_65825.map" model { file = "/net/cci-nas-00/data/ceres_data/9wao_65825/03_2026/9wao_65825.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9wao_65825/03_2026/9wao_65825.cif" } resolution = 3.5 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 ------------------------------------------------------------------------------- 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= 1.000 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 S 12 5.16 5 C 1764 2.51 5 N 468 2.21 5 O 468 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model 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: 2712 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 226 Classifications: {'peptide': 31} Modifications used: {'COO': 1} Link IDs: {'TRANS': 30} Restraints were copied for chains: B, C, D, E, F, G, H, I, J, K, L Time building chain proxies: 0.38, per 1000 atoms: 0.14 Number of scatterers: 2712 At special positions: 0 Unit cell: (54.988, 81.084, 45.668, 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) S 12 16.00 O 468 8.00 N 468 7.00 C 1764 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: 0.18 Conformation dependent library (CDL) restraints added in 118.6 milliseconds 696 Ramachandran restraints generated. 348 Oldfield, 0 Emsley, 348 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 624 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 7 sheets defined 0.0% alpha, 30.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.14 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'E' and resid 18 through 20 removed outlier: 6.354A pdb=" N VAL E 18 " --> pdb=" O PHE G 19 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N VAL A 18 " --> pdb=" O PHE C 19 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N VAL C 18 " --> pdb=" O PHE I 19 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N VAL I 18 " --> pdb=" O PHE K 19 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 30 through 36 removed outlier: 6.866A pdb=" N ILE G 31 " --> pdb=" O ALA E 30 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N ILE E 32 " --> pdb=" O ILE G 31 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N GLY G 33 " --> pdb=" O ILE E 32 " (cutoff:3.500A) removed outlier: 8.959A pdb=" N ILE A 31 " --> pdb=" O ILE G 32 " (cutoff:3.500A) removed outlier: 9.490A pdb=" N LEU G 34 " --> pdb=" O ILE A 31 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N GLY A 33 " --> pdb=" O LEU G 34 " (cutoff:3.500A) removed outlier: 8.277A pdb=" N VAL G 36 " --> pdb=" O GLY A 33 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N MET A 35 " --> pdb=" O VAL G 36 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N ILE C 31 " --> pdb=" O ALA A 30 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N ILE A 32 " --> pdb=" O ILE C 31 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N GLY C 33 " --> pdb=" O ILE A 32 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N ILE I 31 " --> pdb=" O ALA C 30 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N ILE C 32 " --> pdb=" O ILE I 31 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N GLY I 33 " --> pdb=" O ILE C 32 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N ILE K 31 " --> pdb=" O ALA I 30 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ILE I 32 " --> pdb=" O ILE K 31 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N GLY K 33 " --> pdb=" O ILE I 32 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 39 through 40 removed outlier: 6.834A pdb=" N VAL E 39 " --> pdb=" O VAL G 40 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N VAL A 39 " --> pdb=" O VAL C 40 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N VAL C 39 " --> pdb=" O VAL I 40 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N VAL I 39 " --> pdb=" O VAL K 40 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'F' and resid 18 through 20 removed outlier: 6.386A pdb=" N VAL F 18 " --> pdb=" O PHE H 19 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N VAL B 18 " --> pdb=" O PHE D 19 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N VAL D 18 " --> pdb=" O PHE J 19 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N VAL J 18 " --> pdb=" O PHE L 19 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'F' and resid 30 through 36 removed outlier: 6.857A pdb=" N ILE H 31 " --> pdb=" O ALA F 30 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N ILE F 32 " --> pdb=" O ILE H 31 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N GLY H 33 " --> pdb=" O ILE F 32 " (cutoff:3.500A) removed outlier: 8.969A pdb=" N ILE B 31 " --> pdb=" O ILE H 32 " (cutoff:3.500A) removed outlier: 9.489A pdb=" N LEU H 34 " --> pdb=" O ILE B 31 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N GLY B 33 " --> pdb=" O LEU H 34 " (cutoff:3.500A) removed outlier: 8.269A pdb=" N VAL H 36 " --> pdb=" O GLY B 33 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N MET B 35 " --> pdb=" O VAL H 36 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N ILE D 31 " --> pdb=" O ALA B 30 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N ILE B 32 " --> pdb=" O ILE D 31 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N GLY D 33 " --> pdb=" O ILE B 32 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N ILE J 31 " --> pdb=" O ALA D 30 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N ILE D 32 " --> pdb=" O ILE J 31 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N GLY J 33 " --> pdb=" O ILE D 32 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N ILE L 31 " --> pdb=" O ALA J 30 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N ILE J 32 " --> pdb=" O ILE L 31 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N GLY L 33 " --> pdb=" O ILE J 32 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 39 through 40 removed outlier: 6.858A pdb=" N VAL F 39 " --> pdb=" O VAL H 40 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N VAL B 39 " --> pdb=" O VAL D 40 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N VAL D 39 " --> pdb=" O VAL J 40 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N VAL J 39 " --> pdb=" O VAL L 40 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 24 through 27 removed outlier: 8.694A pdb=" N VAL C 24 " --> pdb=" O GLY I 25 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N ASN I 27 " --> pdb=" O VAL C 24 " (cutoff:3.500A) removed outlier: 8.646A pdb=" N SER C 26 " --> pdb=" O ASN I 27 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 30 hydrogen bonds defined for protein. 90 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: 0.38 Time building geometry restraints manager: 0.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 741 1.33 - 1.44: 399 1.44 - 1.56: 1584 1.56 - 1.68: 0 1.68 - 1.80: 24 Bond restraints: 2748 Sorted by residual: bond pdb=" CB VAL B 24 " pdb=" CG1 VAL B 24 " ideal model delta sigma weight residual 1.521 1.472 0.049 3.30e-02 9.18e+02 2.21e+00 bond pdb=" CB VAL F 24 " pdb=" CG1 VAL F 24 " ideal model delta sigma weight residual 1.521 1.472 0.049 3.30e-02 9.18e+02 2.19e+00 bond pdb=" CB VAL L 24 " pdb=" CG1 VAL L 24 " ideal model delta sigma weight residual 1.521 1.472 0.049 3.30e-02 9.18e+02 2.18e+00 bond pdb=" CB VAL E 24 " pdb=" CG1 VAL E 24 " ideal model delta sigma weight residual 1.521 1.472 0.049 3.30e-02 9.18e+02 2.18e+00 bond pdb=" CB VAL C 24 " pdb=" CG1 VAL C 24 " ideal model delta sigma weight residual 1.521 1.472 0.049 3.30e-02 9.18e+02 2.17e+00 ... (remaining 2743 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.48: 3276 1.48 - 2.95: 326 2.95 - 4.43: 58 4.43 - 5.91: 12 5.91 - 7.39: 24 Bond angle restraints: 3696 Sorted by residual: angle pdb=" CA GLN J 15 " pdb=" CB GLN J 15 " pdb=" CG GLN J 15 " ideal model delta sigma weight residual 114.10 120.48 -6.38 2.00e+00 2.50e-01 1.02e+01 angle pdb=" CA GLN D 15 " pdb=" CB GLN D 15 " pdb=" CG GLN D 15 " ideal model delta sigma weight residual 114.10 120.47 -6.37 2.00e+00 2.50e-01 1.01e+01 angle pdb=" CA GLN E 15 " pdb=" CB GLN E 15 " pdb=" CG GLN E 15 " ideal model delta sigma weight residual 114.10 120.47 -6.37 2.00e+00 2.50e-01 1.01e+01 angle pdb=" CA GLN F 15 " pdb=" CB GLN F 15 " pdb=" CG GLN F 15 " ideal model delta sigma weight residual 114.10 120.47 -6.37 2.00e+00 2.50e-01 1.01e+01 angle pdb=" CA GLN L 15 " pdb=" CB GLN L 15 " pdb=" CG GLN L 15 " ideal model delta sigma weight residual 114.10 120.46 -6.36 2.00e+00 2.50e-01 1.01e+01 ... (remaining 3691 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.46: 1296 13.46 - 26.91: 168 26.91 - 40.36: 36 40.36 - 53.82: 24 53.82 - 67.27: 24 Dihedral angle restraints: 1548 sinusoidal: 564 harmonic: 984 Sorted by residual: dihedral pdb=" CA ASP D 23 " pdb=" C ASP D 23 " pdb=" N VAL D 24 " pdb=" CA VAL D 24 " ideal model delta harmonic sigma weight residual 180.00 162.16 17.84 0 5.00e+00 4.00e-02 1.27e+01 dihedral pdb=" CA ASP K 23 " pdb=" C ASP K 23 " pdb=" N VAL K 24 " pdb=" CA VAL K 24 " ideal model delta harmonic sigma weight residual 180.00 162.16 17.84 0 5.00e+00 4.00e-02 1.27e+01 dihedral pdb=" CA ASP C 23 " pdb=" C ASP C 23 " pdb=" N VAL C 24 " pdb=" CA VAL C 24 " ideal model delta harmonic sigma weight residual 180.00 162.17 17.83 0 5.00e+00 4.00e-02 1.27e+01 ... (remaining 1545 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 113 0.029 - 0.059: 155 0.059 - 0.088: 97 0.088 - 0.117: 55 0.117 - 0.147: 24 Chirality restraints: 444 Sorted by residual: chirality pdb=" CB ILE G 41 " pdb=" CA ILE G 41 " pdb=" CG1 ILE G 41 " pdb=" CG2 ILE G 41 " both_signs ideal model delta sigma weight residual False 2.64 2.79 -0.15 2.00e-01 2.50e+01 5.37e-01 chirality pdb=" CB ILE K 41 " pdb=" CA ILE K 41 " pdb=" CG1 ILE K 41 " pdb=" CG2 ILE K 41 " both_signs ideal model delta sigma weight residual False 2.64 2.79 -0.15 2.00e-01 2.50e+01 5.33e-01 chirality pdb=" CB ILE B 41 " pdb=" CA ILE B 41 " pdb=" CG1 ILE B 41 " pdb=" CG2 ILE B 41 " both_signs ideal model delta sigma weight residual False 2.64 2.79 -0.15 2.00e-01 2.50e+01 5.31e-01 ... (remaining 441 not shown) Planarity restraints: 468 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL E 36 " -0.004 2.00e-02 2.50e+03 8.13e-03 6.60e-01 pdb=" C VAL E 36 " 0.014 2.00e-02 2.50e+03 pdb=" O VAL E 36 " -0.005 2.00e-02 2.50e+03 pdb=" N GLY E 37 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL J 36 " 0.004 2.00e-02 2.50e+03 7.91e-03 6.25e-01 pdb=" C VAL J 36 " -0.014 2.00e-02 2.50e+03 pdb=" O VAL J 36 " 0.005 2.00e-02 2.50e+03 pdb=" N GLY J 37 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 36 " -0.004 2.00e-02 2.50e+03 7.73e-03 5.97e-01 pdb=" C VAL A 36 " 0.013 2.00e-02 2.50e+03 pdb=" O VAL A 36 " -0.005 2.00e-02 2.50e+03 pdb=" N GLY A 37 " -0.004 2.00e-02 2.50e+03 ... (remaining 465 not shown) Histogram of nonbonded interaction distances: 2.55 - 3.02: 1627 3.02 - 3.49: 2606 3.49 - 3.96: 4141 3.96 - 4.43: 4922 4.43 - 4.90: 9101 Nonbonded interactions: 22397 Sorted by model distance: nonbonded pdb=" C SER E 26 " pdb=" OG SER E 26 " model vdw 2.545 2.616 nonbonded pdb=" C SER L 26 " pdb=" OG SER L 26 " model vdw 2.545 2.616 nonbonded pdb=" C SER J 26 " pdb=" OG SER J 26 " model vdw 2.546 2.616 nonbonded pdb=" C SER F 26 " pdb=" OG SER F 26 " model vdw 2.546 2.616 nonbonded pdb=" C SER I 26 " pdb=" OG SER I 26 " model vdw 2.546 2.616 ... (remaining 22392 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 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.290 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: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.470 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 6.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 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 : 0.011 0.049 2748 Z= 0.469 Angle : 1.096 7.386 3696 Z= 0.584 Chirality : 0.064 0.147 444 Planarity : 0.003 0.008 468 Dihedral : 17.431 67.274 924 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 25.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.79 % Favored : 86.21 % Rotamer: Outliers : 0.00 % Allowed : 32.97 % Favored : 67.03 % 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: -2.50 (0.41), residues: 348 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.90 (0.31), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.004 0.002 PHE L 19 HIS 0.001 0.001 HIS I 13 Details of bonding type rmsd covalent geometry : bond 0.01089 ( 2748) covalent geometry : angle 1.09556 ( 3696) hydrogen bonds : bond 0.22784 ( 30) hydrogen bonds : angle 7.80211 ( 90) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 696 Ramachandran restraints generated. 348 Oldfield, 0 Emsley, 348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 696 Ramachandran restraints generated. 348 Oldfield, 0 Emsley, 348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 0.102 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 77 average time/residue: 0.0607 time to fit residues: 5.4848 Evaluate side-chains 63 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 63 time to evaluate : 0.085 ------------------------------------------------------------------------------- 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: 0.9990 chunk 26 optimal weight: 0.9990 chunk 2 optimal weight: 0.7980 chunk 16 optimal weight: 4.9990 chunk 32 optimal weight: 8.9990 chunk 31 optimal weight: 30.0000 chunk 25 optimal weight: 8.9990 chunk 19 optimal weight: 6.9990 chunk 30 optimal weight: 2.9990 chunk 22 optimal weight: 5.9990 chunk 13 optimal weight: 3.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.135055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.111432 restraints weight = 3532.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.115259 restraints weight = 1863.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.117888 restraints weight = 1281.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.119711 restraints weight = 994.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.120873 restraints weight = 830.489| |-----------------------------------------------------------------------------| r_work (final): 0.3757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.1682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.014 2748 Z= 0.116 Angle : 0.596 4.726 3696 Z= 0.332 Chirality : 0.060 0.133 444 Planarity : 0.002 0.010 468 Dihedral : 12.607 68.568 372 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 10.14 % Allowed : 22.83 % Favored : 67.03 % 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: -1.63 (0.43), residues: 348 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.23 (0.33), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.003 0.001 PHE G 20 HIS 0.001 0.000 HIS C 14 Details of bonding type rmsd covalent geometry : bond 0.00253 ( 2748) covalent geometry : angle 0.59648 ( 3696) hydrogen bonds : bond 0.04420 ( 30) hydrogen bonds : angle 6.59179 ( 90) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 696 Ramachandran restraints generated. 348 Oldfield, 0 Emsley, 348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 696 Ramachandran restraints generated. 348 Oldfield, 0 Emsley, 348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 76 time to evaluate : 0.095 Fit side-chains REVERT: A 15 GLN cc_start: 0.8069 (tm-30) cc_final: 0.7835 (tm-30) REVERT: B 15 GLN cc_start: 0.8029 (tm-30) cc_final: 0.7791 (tm-30) REVERT: E 35 MET cc_start: 0.7458 (ptt) cc_final: 0.7100 (ttp) REVERT: F 35 MET cc_start: 0.7501 (ptt) cc_final: 0.7112 (ttp) REVERT: I 15 GLN cc_start: 0.8566 (tm-30) cc_final: 0.8029 (tm-30) REVERT: J 15 GLN cc_start: 0.8622 (tm-30) cc_final: 0.8074 (tm-30) REVERT: K 15 GLN cc_start: 0.8716 (tm-30) cc_final: 0.7735 (tm-30) REVERT: L 15 GLN cc_start: 0.8726 (tm-30) cc_final: 0.7710 (tm-30) outliers start: 28 outliers final: 16 residues processed: 91 average time/residue: 0.0356 time to fit residues: 4.3228 Evaluate side-chains 83 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 67 time to evaluate : 0.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain I residue 36 VAL Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain K residue 26 SER Chi-restraints excluded: chain L residue 26 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 18 optimal weight: 7.9990 chunk 2 optimal weight: 0.8980 chunk 1 optimal weight: 5.9990 chunk 0 optimal weight: 9.9990 chunk 17 optimal weight: 9.9990 chunk 4 optimal weight: 8.9990 chunk 20 optimal weight: 5.9990 chunk 35 optimal weight: 7.9990 chunk 3 optimal weight: 10.0000 chunk 15 optimal weight: 10.0000 chunk 33 optimal weight: 7.9990 overall best weight: 5.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.130437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.106149 restraints weight = 3610.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.109598 restraints weight = 1890.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.111863 restraints weight = 1325.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.113356 restraints weight = 1056.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.114023 restraints weight = 906.645| |-----------------------------------------------------------------------------| r_work (final): 0.3746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.1969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 2748 Z= 0.235 Angle : 0.632 5.480 3696 Z= 0.334 Chirality : 0.059 0.146 444 Planarity : 0.002 0.013 468 Dihedral : 11.897 72.380 372 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 10.51 % Allowed : 23.19 % Favored : 66.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.74 (0.42), residues: 348 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.32 (0.32), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.006 0.001 PHE L 19 HIS 0.002 0.000 HIS E 13 Details of bonding type rmsd covalent geometry : bond 0.00577 ( 2748) covalent geometry : angle 0.63195 ( 3696) hydrogen bonds : bond 0.05252 ( 30) hydrogen bonds : angle 6.49946 ( 90) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 696 Ramachandran restraints generated. 348 Oldfield, 0 Emsley, 348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 696 Ramachandran restraints generated. 348 Oldfield, 0 Emsley, 348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 67 time to evaluate : 0.110 Fit side-chains REVERT: A 15 GLN cc_start: 0.8385 (tm-30) cc_final: 0.7942 (tm-30) REVERT: G 15 GLN cc_start: 0.7919 (tm-30) cc_final: 0.7668 (tm-30) REVERT: H 15 GLN cc_start: 0.7936 (tm-30) cc_final: 0.7666 (tm-30) REVERT: I 15 GLN cc_start: 0.8747 (tm-30) cc_final: 0.8060 (tm-30) REVERT: J 15 GLN cc_start: 0.8856 (tm-30) cc_final: 0.8233 (tm-30) REVERT: K 15 GLN cc_start: 0.8887 (tm-30) cc_final: 0.8131 (tm-30) REVERT: L 15 GLN cc_start: 0.8900 (tm-30) cc_final: 0.8136 (tm-30) outliers start: 29 outliers final: 21 residues processed: 86 average time/residue: 0.0364 time to fit residues: 4.1315 Evaluate side-chains 85 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 64 time to evaluate : 0.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain I residue 26 SER Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain K residue 26 SER Chi-restraints excluded: chain L residue 26 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 2 optimal weight: 5.9990 chunk 25 optimal weight: 20.0000 chunk 16 optimal weight: 9.9990 chunk 32 optimal weight: 0.9980 chunk 21 optimal weight: 6.9990 chunk 14 optimal weight: 10.0000 chunk 4 optimal weight: 6.9990 chunk 28 optimal weight: 10.0000 chunk 8 optimal weight: 5.9990 chunk 6 optimal weight: 7.9990 chunk 17 optimal weight: 8.9990 overall best weight: 5.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 27 ASN ** E 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.132057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.108012 restraints weight = 3483.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.111898 restraints weight = 1841.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.114452 restraints weight = 1260.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.116166 restraints weight = 983.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.117383 restraints weight = 828.531| |-----------------------------------------------------------------------------| r_work (final): 0.3808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.2202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 2748 Z= 0.217 Angle : 0.614 5.673 3696 Z= 0.325 Chirality : 0.059 0.137 444 Planarity : 0.002 0.009 468 Dihedral : 11.395 73.715 372 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 13.04 % Allowed : 19.93 % Favored : 67.03 % 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: -1.82 (0.42), residues: 348 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.38 (0.32), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.005 0.001 PHE I 19 HIS 0.001 0.001 HIS I 14 Details of bonding type rmsd covalent geometry : bond 0.00525 ( 2748) covalent geometry : angle 0.61433 ( 3696) hydrogen bonds : bond 0.05208 ( 30) hydrogen bonds : angle 6.58186 ( 90) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 696 Ramachandran restraints generated. 348 Oldfield, 0 Emsley, 348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 696 Ramachandran restraints generated. 348 Oldfield, 0 Emsley, 348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 61 time to evaluate : 0.066 Fit side-chains REVERT: F 15 GLN cc_start: 0.7580 (tm-30) cc_final: 0.7364 (tt0) REVERT: G 15 GLN cc_start: 0.7786 (tm-30) cc_final: 0.6575 (tm-30) REVERT: H 15 GLN cc_start: 0.7743 (tm-30) cc_final: 0.6627 (tm-30) REVERT: I 15 GLN cc_start: 0.8724 (tm-30) cc_final: 0.7899 (tm-30) REVERT: J 15 GLN cc_start: 0.8806 (tm-30) cc_final: 0.8046 (tm-30) REVERT: K 15 GLN cc_start: 0.8838 (tm-30) cc_final: 0.7984 (tm-30) REVERT: L 15 GLN cc_start: 0.8849 (tm-30) cc_final: 0.7986 (tm-30) outliers start: 36 outliers final: 23 residues processed: 85 average time/residue: 0.0282 time to fit residues: 3.3214 Evaluate side-chains 84 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 61 time to evaluate : 0.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 26 SER Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain K residue 26 SER Chi-restraints excluded: chain L residue 26 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 24 optimal weight: 9.9990 chunk 17 optimal weight: 6.9990 chunk 5 optimal weight: 8.9990 chunk 3 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 8 optimal weight: 6.9990 chunk 14 optimal weight: 10.0000 chunk 35 optimal weight: 8.9990 chunk 34 optimal weight: 0.8980 chunk 18 optimal weight: 9.9990 chunk 11 optimal weight: 5.9990 overall best weight: 5.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.130238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.105406 restraints weight = 3486.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.109045 restraints weight = 1838.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.111454 restraints weight = 1289.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.113058 restraints weight = 1020.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.114092 restraints weight = 869.795| |-----------------------------------------------------------------------------| r_work (final): 0.3748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.2330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 2748 Z= 0.236 Angle : 0.630 5.918 3696 Z= 0.330 Chirality : 0.059 0.135 444 Planarity : 0.002 0.009 468 Dihedral : 11.087 74.241 372 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 13.77 % Allowed : 18.12 % Favored : 68.12 % 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: -1.89 (0.42), residues: 348 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.43 (0.32), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.006 0.001 PHE L 19 HIS 0.002 0.001 HIS F 13 Details of bonding type rmsd covalent geometry : bond 0.00570 ( 2748) covalent geometry : angle 0.62960 ( 3696) hydrogen bonds : bond 0.05046 ( 30) hydrogen bonds : angle 6.58990 ( 90) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 696 Ramachandran restraints generated. 348 Oldfield, 0 Emsley, 348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 696 Ramachandran restraints generated. 348 Oldfield, 0 Emsley, 348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 62 time to evaluate : 0.100 Fit side-chains REVERT: C 15 GLN cc_start: 0.8571 (tm-30) cc_final: 0.7425 (tm-30) REVERT: D 15 GLN cc_start: 0.8570 (tm-30) cc_final: 0.7440 (tm-30) REVERT: F 15 GLN cc_start: 0.7640 (tm-30) cc_final: 0.6996 (tm-30) REVERT: G 15 GLN cc_start: 0.7903 (tm-30) cc_final: 0.6907 (tm-30) REVERT: H 15 GLN cc_start: 0.7870 (tm-30) cc_final: 0.6921 (tm-30) REVERT: I 15 GLN cc_start: 0.8830 (tm-30) cc_final: 0.8037 (tm-30) REVERT: J 15 GLN cc_start: 0.8815 (tm-30) cc_final: 0.8223 (tm-30) REVERT: K 15 GLN cc_start: 0.8889 (tm-30) cc_final: 0.8055 (tm-30) REVERT: L 15 GLN cc_start: 0.8898 (tm-30) cc_final: 0.8067 (tm-30) outliers start: 38 outliers final: 31 residues processed: 84 average time/residue: 0.0280 time to fit residues: 3.2850 Evaluate side-chains 91 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 60 time to evaluate : 0.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 GLU Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain C residue 35 MET Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain D residue 35 MET Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 26 SER Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 26 SER Chi-restraints excluded: chain L residue 12 VAL Chi-restraints excluded: chain L residue 26 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 13 optimal weight: 9.9990 chunk 33 optimal weight: 7.9990 chunk 35 optimal weight: 7.9990 chunk 11 optimal weight: 9.9990 chunk 25 optimal weight: 20.0000 chunk 30 optimal weight: 7.9990 chunk 31 optimal weight: 7.9990 chunk 12 optimal weight: 10.0000 chunk 14 optimal weight: 9.9990 chunk 23 optimal weight: 5.9990 chunk 34 optimal weight: 0.5980 overall best weight: 6.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 13 HIS ** K 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.130240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.105300 restraints weight = 3543.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.109108 restraints weight = 1867.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.111489 restraints weight = 1292.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.113158 restraints weight = 1025.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.114243 restraints weight = 873.404| |-----------------------------------------------------------------------------| r_work (final): 0.3746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.2468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 2748 Z= 0.240 Angle : 0.636 6.175 3696 Z= 0.331 Chirality : 0.060 0.136 444 Planarity : 0.002 0.010 468 Dihedral : 10.885 74.612 372 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 12.68 % Allowed : 19.20 % Favored : 68.12 % 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: -1.93 (0.41), residues: 348 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.47 (0.31), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.006 0.001 PHE L 19 HIS 0.002 0.001 HIS B 14 Details of bonding type rmsd covalent geometry : bond 0.00579 ( 2748) covalent geometry : angle 0.63606 ( 3696) hydrogen bonds : bond 0.05278 ( 30) hydrogen bonds : angle 6.76291 ( 90) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 696 Ramachandran restraints generated. 348 Oldfield, 0 Emsley, 348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 696 Ramachandran restraints generated. 348 Oldfield, 0 Emsley, 348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 58 time to evaluate : 0.105 Fit side-chains REVERT: C 15 GLN cc_start: 0.8575 (tm-30) cc_final: 0.7414 (tm-30) REVERT: D 15 GLN cc_start: 0.8576 (tm-30) cc_final: 0.7429 (tm-30) REVERT: F 15 GLN cc_start: 0.7632 (tm-30) cc_final: 0.7061 (tm-30) REVERT: G 15 GLN cc_start: 0.7890 (tm-30) cc_final: 0.6877 (tm-30) REVERT: H 15 GLN cc_start: 0.7877 (tm-30) cc_final: 0.6959 (tm-30) REVERT: I 15 GLN cc_start: 0.8833 (tm-30) cc_final: 0.8093 (tm-30) REVERT: J 15 GLN cc_start: 0.8822 (tm-30) cc_final: 0.8248 (tm-30) REVERT: K 15 GLN cc_start: 0.8890 (tm-30) cc_final: 0.8167 (tm-30) REVERT: L 15 GLN cc_start: 0.8901 (tm-30) cc_final: 0.8181 (tm-30) outliers start: 35 outliers final: 34 residues processed: 79 average time/residue: 0.0294 time to fit residues: 3.2446 Evaluate side-chains 92 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 58 time to evaluate : 0.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 GLU Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain A residue 35 MET Chi-restraints excluded: chain B residue 22 GLU Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain B residue 35 MET Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain C residue 35 MET Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain D residue 35 MET Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 26 SER Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 26 SER Chi-restraints excluded: chain L residue 12 VAL Chi-restraints excluded: chain L residue 26 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 34 optimal weight: 20.0000 chunk 19 optimal weight: 9.9990 chunk 14 optimal weight: 7.9990 chunk 9 optimal weight: 10.0000 chunk 11 optimal weight: 6.9990 chunk 1 optimal weight: 6.9990 chunk 3 optimal weight: 9.9990 chunk 28 optimal weight: 5.9990 chunk 10 optimal weight: 9.9990 chunk 31 optimal weight: 30.0000 chunk 8 optimal weight: 10.0000 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.128206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.103414 restraints weight = 3545.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.107008 restraints weight = 1873.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.109325 restraints weight = 1317.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.110876 restraints weight = 1051.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.111630 restraints weight = 897.433| |-----------------------------------------------------------------------------| r_work (final): 0.3716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.2516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.051 2748 Z= 0.291 Angle : 0.677 6.603 3696 Z= 0.350 Chirality : 0.060 0.139 444 Planarity : 0.002 0.009 468 Dihedral : 10.621 75.651 372 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 13.77 % Allowed : 19.20 % Favored : 67.03 % 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: -2.04 (0.41), residues: 348 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.55 (0.31), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.008 0.001 PHE K 19 HIS 0.002 0.001 HIS F 13 Details of bonding type rmsd covalent geometry : bond 0.00702 ( 2748) covalent geometry : angle 0.67717 ( 3696) hydrogen bonds : bond 0.05273 ( 30) hydrogen bonds : angle 6.84189 ( 90) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 696 Ramachandran restraints generated. 348 Oldfield, 0 Emsley, 348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 696 Ramachandran restraints generated. 348 Oldfield, 0 Emsley, 348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 65 time to evaluate : 0.131 Fit side-chains REVERT: F 15 GLN cc_start: 0.7674 (tm-30) cc_final: 0.6976 (tm-30) REVERT: G 15 GLN cc_start: 0.7907 (tm-30) cc_final: 0.6923 (tm-30) REVERT: H 15 GLN cc_start: 0.7898 (tm-30) cc_final: 0.6999 (tm-30) REVERT: I 15 GLN cc_start: 0.8840 (tm-30) cc_final: 0.8119 (tm-30) REVERT: J 15 GLN cc_start: 0.8824 (tm-30) cc_final: 0.8241 (tm-30) REVERT: K 15 GLN cc_start: 0.8897 (tm-30) cc_final: 0.8149 (tm-30) REVERT: L 15 GLN cc_start: 0.8906 (tm-30) cc_final: 0.8151 (tm-30) outliers start: 38 outliers final: 32 residues processed: 88 average time/residue: 0.0324 time to fit residues: 3.9727 Evaluate side-chains 95 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 63 time to evaluate : 0.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 GLU Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain B residue 22 GLU Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain C residue 35 MET Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain D residue 35 MET Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 26 SER Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 26 SER Chi-restraints excluded: chain L residue 12 VAL Chi-restraints excluded: chain L residue 26 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 14 optimal weight: 5.9990 chunk 31 optimal weight: 3.9990 chunk 1 optimal weight: 10.0000 chunk 28 optimal weight: 6.9990 chunk 10 optimal weight: 8.9990 chunk 16 optimal weight: 6.9990 chunk 25 optimal weight: 8.9990 chunk 32 optimal weight: 4.9990 chunk 26 optimal weight: 5.9990 chunk 4 optimal weight: 0.9990 chunk 5 optimal weight: 7.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.132351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.107591 restraints weight = 3562.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.111362 restraints weight = 1905.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.113708 restraints weight = 1325.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.115311 restraints weight = 1053.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.116461 restraints weight = 899.735| |-----------------------------------------------------------------------------| r_work (final): 0.3777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 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 : 0.004 0.040 2748 Z= 0.183 Angle : 0.628 6.294 3696 Z= 0.323 Chirality : 0.060 0.145 444 Planarity : 0.002 0.016 468 Dihedral : 10.219 73.801 372 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 12.68 % Allowed : 18.84 % Favored : 68.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.86 (0.42), residues: 348 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.41 (0.32), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.004 0.001 PHE K 19 HIS 0.001 0.001 HIS B 14 Details of bonding type rmsd covalent geometry : bond 0.00438 ( 2748) covalent geometry : angle 0.62773 ( 3696) hydrogen bonds : bond 0.05251 ( 30) hydrogen bonds : angle 6.79350 ( 90) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 696 Ramachandran restraints generated. 348 Oldfield, 0 Emsley, 348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 696 Ramachandran restraints generated. 348 Oldfield, 0 Emsley, 348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 59 time to evaluate : 0.104 Fit side-chains REVERT: C 15 GLN cc_start: 0.8584 (tm-30) cc_final: 0.7531 (tm-30) REVERT: D 15 GLN cc_start: 0.8586 (tm-30) cc_final: 0.7541 (tm-30) REVERT: F 15 GLN cc_start: 0.7590 (tm-30) cc_final: 0.7305 (tm-30) REVERT: G 15 GLN cc_start: 0.7899 (tm-30) cc_final: 0.6943 (tm-30) REVERT: H 15 GLN cc_start: 0.7866 (tm-30) cc_final: 0.7016 (tm-30) REVERT: I 15 GLN cc_start: 0.8833 (tm-30) cc_final: 0.8101 (tm-30) REVERT: J 15 GLN cc_start: 0.8808 (tm-30) cc_final: 0.8170 (tm-30) REVERT: K 15 GLN cc_start: 0.8898 (tm-30) cc_final: 0.8166 (tm-30) REVERT: L 15 GLN cc_start: 0.8909 (tm-30) cc_final: 0.8175 (tm-30) outliers start: 35 outliers final: 31 residues processed: 80 average time/residue: 0.0295 time to fit residues: 3.3280 Evaluate side-chains 90 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 59 time to evaluate : 0.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 GLU Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain B residue 22 GLU Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain B residue 35 MET Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain C residue 35 MET Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain D residue 35 MET Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 26 SER Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 26 SER Chi-restraints excluded: chain L residue 12 VAL Chi-restraints excluded: chain L residue 26 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 19 optimal weight: 10.0000 chunk 20 optimal weight: 8.9990 chunk 9 optimal weight: 9.9990 chunk 31 optimal weight: 20.0000 chunk 32 optimal weight: 0.9980 chunk 18 optimal weight: 9.9990 chunk 11 optimal weight: 10.0000 chunk 6 optimal weight: 7.9990 chunk 16 optimal weight: 20.0000 chunk 7 optimal weight: 20.0000 chunk 2 optimal weight: 2.9990 overall best weight: 6.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.129760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.104883 restraints weight = 3652.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.108653 restraints weight = 1903.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.111027 restraints weight = 1314.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.112602 restraints weight = 1039.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.113725 restraints weight = 885.734| |-----------------------------------------------------------------------------| r_work (final): 0.3749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 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 : 0.006 0.046 2748 Z= 0.246 Angle : 0.662 6.311 3696 Z= 0.341 Chirality : 0.060 0.143 444 Planarity : 0.002 0.015 468 Dihedral : 10.165 74.773 372 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 12.32 % Allowed : 20.29 % Favored : 67.39 % 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: -1.89 (0.41), residues: 348 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.43 (0.32), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.006 0.001 PHE K 19 HIS 0.002 0.001 HIS I 14 Details of bonding type rmsd covalent geometry : bond 0.00593 ( 2748) covalent geometry : angle 0.66226 ( 3696) hydrogen bonds : bond 0.05417 ( 30) hydrogen bonds : angle 6.89184 ( 90) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 696 Ramachandran restraints generated. 348 Oldfield, 0 Emsley, 348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 696 Ramachandran restraints generated. 348 Oldfield, 0 Emsley, 348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 63 time to evaluate : 0.105 Fit side-chains REVERT: C 15 GLN cc_start: 0.8587 (tm-30) cc_final: 0.7428 (tm-30) REVERT: D 15 GLN cc_start: 0.8593 (tm-30) cc_final: 0.7442 (tm-30) REVERT: F 15 GLN cc_start: 0.7659 (tm-30) cc_final: 0.7355 (tm-30) REVERT: G 15 GLN cc_start: 0.7884 (tm-30) cc_final: 0.6922 (tm-30) REVERT: H 15 GLN cc_start: 0.7880 (tm-30) cc_final: 0.6989 (tm-30) REVERT: I 15 GLN cc_start: 0.8834 (tm-30) cc_final: 0.8082 (tm-30) REVERT: J 15 GLN cc_start: 0.8811 (tm-30) cc_final: 0.8244 (tm-30) REVERT: K 15 GLN cc_start: 0.8886 (tm-30) cc_final: 0.8092 (tm-30) REVERT: L 15 GLN cc_start: 0.8890 (tm-30) cc_final: 0.8096 (tm-30) outliers start: 34 outliers final: 27 residues processed: 83 average time/residue: 0.0299 time to fit residues: 3.4557 Evaluate side-chains 90 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 63 time to evaluate : 0.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain D residue 35 MET Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 26 SER Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 26 SER Chi-restraints excluded: chain L residue 12 VAL Chi-restraints excluded: chain L residue 26 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 31 optimal weight: 30.0000 chunk 10 optimal weight: 6.9990 chunk 32 optimal weight: 9.9990 chunk 13 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 1 optimal weight: 9.9990 chunk 35 optimal weight: 8.9990 chunk 15 optimal weight: 10.0000 chunk 3 optimal weight: 10.0000 chunk 29 optimal weight: 5.9990 chunk 18 optimal weight: 10.0000 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.128692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.103747 restraints weight = 3622.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.107510 restraints weight = 1911.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.109812 restraints weight = 1326.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.111371 restraints weight = 1055.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.112317 restraints weight = 900.316| |-----------------------------------------------------------------------------| r_work (final): 0.3732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.2638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.050 2748 Z= 0.287 Angle : 0.695 6.495 3696 Z= 0.359 Chirality : 0.061 0.138 444 Planarity : 0.002 0.015 468 Dihedral : 10.228 76.102 372 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 10.51 % Allowed : 22.10 % Favored : 67.39 % 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: -1.95 (0.41), residues: 348 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.48 (0.31), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.008 0.001 PHE K 19 HIS 0.002 0.001 HIS F 13 Details of bonding type rmsd covalent geometry : bond 0.00694 ( 2748) covalent geometry : angle 0.69492 ( 3696) hydrogen bonds : bond 0.05694 ( 30) hydrogen bonds : angle 7.01224 ( 90) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 696 Ramachandran restraints generated. 348 Oldfield, 0 Emsley, 348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 696 Ramachandran restraints generated. 348 Oldfield, 0 Emsley, 348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 62 time to evaluate : 0.099 Fit side-chains REVERT: F 15 GLN cc_start: 0.7676 (tm-30) cc_final: 0.7383 (tm-30) REVERT: G 15 GLN cc_start: 0.7903 (tm-30) cc_final: 0.6938 (tm-30) REVERT: H 15 GLN cc_start: 0.7894 (tm-30) cc_final: 0.7006 (tm-30) REVERT: I 15 GLN cc_start: 0.8838 (tm-30) cc_final: 0.8110 (tm-30) REVERT: J 15 GLN cc_start: 0.8811 (tm-30) cc_final: 0.8233 (tm-30) REVERT: K 15 GLN cc_start: 0.8901 (tm-30) cc_final: 0.8123 (tm-30) REVERT: L 15 GLN cc_start: 0.8913 (tm-30) cc_final: 0.8128 (tm-30) outliers start: 29 outliers final: 26 residues processed: 80 average time/residue: 0.0290 time to fit residues: 3.2440 Evaluate side-chains 88 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 62 time to evaluate : 0.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 26 SER Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 26 SER Chi-restraints excluded: chain L residue 12 VAL Chi-restraints excluded: chain L residue 26 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 16 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 5 optimal weight: 0.0060 chunk 9 optimal weight: 9.9990 chunk 31 optimal weight: 20.0000 chunk 10 optimal weight: 9.9990 chunk 25 optimal weight: 5.9990 chunk 1 optimal weight: 9.9990 chunk 14 optimal weight: 0.9990 chunk 32 optimal weight: 0.0670 chunk 22 optimal weight: 8.9990 overall best weight: 3.2140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.134147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.109788 restraints weight = 3492.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.113528 restraints weight = 1863.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.115974 restraints weight = 1297.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.117626 restraints weight = 1018.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.118716 restraints weight = 864.806| |-----------------------------------------------------------------------------| r_work (final): 0.3818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.2814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 2748 Z= 0.148 Angle : 0.616 6.459 3696 Z= 0.319 Chirality : 0.061 0.169 444 Planarity : 0.002 0.014 468 Dihedral : 9.555 72.695 372 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 9.42 % Allowed : 23.55 % Favored : 67.03 % 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: -1.78 (0.42), residues: 348 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.35 (0.32), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.003 0.001 PHE L 19 HIS 0.001 0.000 HIS C 14 Details of bonding type rmsd covalent geometry : bond 0.00354 ( 2748) covalent geometry : angle 0.61570 ( 3696) hydrogen bonds : bond 0.05648 ( 30) hydrogen bonds : angle 6.84905 ( 90) =============================================================================== Job complete usr+sys time: 529.41 seconds wall clock time: 9 minutes 47.02 seconds (587.02 seconds total)