Starting phenix.real_space_refine on Tue Aug 4 12:03:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9w9s_65787/08_2026/9w9s_65787.cif Found real_map, /net/cci-nas-00/data/ceres_data/9w9s_65787/08_2026/9w9s_65787.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.61 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9w9s_65787/08_2026/9w9s_65787.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9w9s_65787/08_2026/9w9s_65787.map" model { file = "/net/cci-nas-00/data/ceres_data/9w9s_65787/08_2026/9w9s_65787.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9w9s_65787/08_2026/9w9s_65787.cif" } resolution = 2.61 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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 3 5.16 5 C 1389 2.51 5 N 351 2.21 5 O 402 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 2145 Number of models: 1 Model: "" Number of chains: 1 Chain: "B" Number of atoms: 715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 715 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 4, 'TRANS': 86} Chain breaks: 1 Restraints were copied for chains: A, C Time building chain proxies: 0.71, per 1000 atoms: 0.33 Number of scatterers: 2145 At special positions: 0 Unit cell: (66.03, 87.42, 32.55, 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 3 16.00 O 402 8.00 N 351 7.00 C 1389 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 93.3 milliseconds 522 Ramachandran restraints generated. 261 Oldfield, 0 Emsley, 261 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 522 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 10 sheets defined 0.0% alpha, 50.5% 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 'A' and resid 13 through 16 removed outlier: 6.464A pdb=" N VAL B 14 " --> pdb=" O LYS A 15 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 19 through 21 removed outlier: 6.460A pdb=" N VAL B 20 " --> pdb=" O ARG A 21 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 25 through 34 removed outlier: 6.324A pdb=" N ALA B 25 " --> pdb=" O ILE C 26 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N VAL C 28 " --> pdb=" O ALA B 25 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N ASN B 27 " --> pdb=" O VAL C 28 " (cutoff:3.500A) removed outlier: 7.702A pdb=" N VAL C 30 " --> pdb=" O ASN B 27 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N ALA B 29 " --> pdb=" O VAL C 30 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N VAL C 32 " --> pdb=" O ALA B 29 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N HIS B 31 " --> pdb=" O VAL C 32 " (cutoff:3.500A) removed outlier: 8.040A pdb=" N ARG C 34 " --> pdb=" O HIS B 31 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N PHE B 33 " --> pdb=" O ARG C 34 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 60 through 62 removed outlier: 6.402A pdb=" N THR B 60 " --> pdb=" O GLU C 61 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 65 through 68 removed outlier: 8.715A pdb=" N GLU B 66 " --> pdb=" O GLY A 67 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N ILE C 68 " --> pdb=" O GLY B 67 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 71 through 73 removed outlier: 6.283A pdb=" N GLU B 72 " --> pdb=" O ILE A 73 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 76 through 80 removed outlier: 9.263A pdb=" N LYS B 76 " --> pdb=" O SER A 77 " (cutoff:3.500A) removed outlier: 9.651A pdb=" N TRP A 79 " --> pdb=" O LYS B 76 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N TYR B 78 " --> pdb=" O TRP A 79 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N SER B 77 " --> pdb=" O LYS C 76 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N TYR C 78 " --> pdb=" O SER B 77 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 89 through 99 removed outlier: 7.135A pdb=" N HIS B 90 " --> pdb=" O GLU A 89 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N GLU B 89 " --> pdb=" O HIS C 90 " (cutoff:3.500A) removed outlier: 8.721A pdb=" N GLU C 92 " --> pdb=" O GLU B 89 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N ALA B 91 " --> pdb=" O GLU C 92 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N VAL C 94 " --> pdb=" O ALA B 91 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N VAL B 93 " --> pdb=" O VAL C 94 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N THR C 96 " --> pdb=" O VAL B 93 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N PHE B 95 " --> pdb=" O THR C 96 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N ASN C 98 " --> pdb=" O PHE B 95 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N SER B 97 " --> pdb=" O ASN C 98 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 103 through 110 removed outlier: 8.872A pdb=" N ARG B 103 " --> pdb=" O ARG A 104 " (cutoff:3.500A) removed outlier: 9.890A pdb=" N THR A 106 " --> pdb=" O ARG B 103 " (cutoff:3.500A) removed outlier: 9.139A pdb=" N TYR B 105 " --> pdb=" O THR A 106 " (cutoff:3.500A) removed outlier: 10.030A pdb=" N ALA A 108 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ILE B 107 " --> pdb=" O ALA A 108 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N LEU A 110 " --> pdb=" O ILE B 107 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N ALA B 109 " --> pdb=" O LEU A 110 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N ARG B 104 " --> pdb=" O ARG C 103 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N TYR C 105 " --> pdb=" O ARG B 104 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N THR B 106 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N ILE C 107 " --> pdb=" O THR B 106 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N ALA B 108 " --> pdb=" O ILE C 107 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 118 through 122 41 hydrogen bonds defined for protein. 123 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: 0.19 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: 1.23 - 1.34: 666 1.34 - 1.46: 369 1.46 - 1.57: 1155 1.57 - 1.69: 0 1.69 - 1.80: 6 Bond restraints: 2196 Sorted by residual: bond pdb=" C VAL A 14 " pdb=" O VAL A 14 " ideal model delta sigma weight residual 1.238 1.229 0.008 1.10e-02 8.26e+03 5.90e-01 bond pdb=" N GLY B 83 " pdb=" CA GLY B 83 " ideal model delta sigma weight residual 1.455 1.447 0.007 1.05e-02 9.07e+03 4.94e-01 bond pdb=" N TYR B 78 " pdb=" CA TYR B 78 " ideal model delta sigma weight residual 1.460 1.468 -0.008 1.22e-02 6.72e+03 4.84e-01 bond pdb=" N TYR A 78 " pdb=" CA TYR A 78 " ideal model delta sigma weight residual 1.460 1.468 -0.008 1.22e-02 6.72e+03 4.56e-01 bond pdb=" C VAL C 14 " pdb=" O VAL C 14 " ideal model delta sigma weight residual 1.238 1.230 0.007 1.10e-02 8.26e+03 4.55e-01 ... (remaining 2191 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.07: 2721 1.07 - 2.13: 207 2.13 - 3.20: 42 3.20 - 4.26: 12 4.26 - 5.33: 6 Bond angle restraints: 2988 Sorted by residual: angle pdb=" N VAL A 16 " pdb=" CA VAL A 16 " pdb=" C VAL A 16 " ideal model delta sigma weight residual 107.77 112.71 -4.94 1.48e+00 4.57e-01 1.11e+01 angle pdb=" N VAL B 16 " pdb=" CA VAL B 16 " pdb=" C VAL B 16 " ideal model delta sigma weight residual 107.77 112.70 -4.93 1.48e+00 4.57e-01 1.11e+01 angle pdb=" N VAL C 16 " pdb=" CA VAL C 16 " pdb=" C VAL C 16 " ideal model delta sigma weight residual 107.77 112.70 -4.93 1.48e+00 4.57e-01 1.11e+01 angle pdb=" CA TYR C 114 " pdb=" CB TYR C 114 " pdb=" CG TYR C 114 " ideal model delta sigma weight residual 113.90 117.76 -3.86 1.80e+00 3.09e-01 4.60e+00 angle pdb=" N HIS B 88 " pdb=" CA HIS B 88 " pdb=" C HIS B 88 " ideal model delta sigma weight residual 111.14 113.45 -2.31 1.08e+00 8.57e-01 4.59e+00 ... (remaining 2983 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.74: 1155 17.74 - 35.47: 93 35.47 - 53.20: 45 53.20 - 70.94: 3 70.94 - 88.67: 3 Dihedral angle restraints: 1299 sinusoidal: 495 harmonic: 804 Sorted by residual: dihedral pdb=" CA ILE C 26 " pdb=" C ILE C 26 " pdb=" N ASN C 27 " pdb=" CA ASN C 27 " ideal model delta harmonic sigma weight residual 180.00 162.61 17.39 0 5.00e+00 4.00e-02 1.21e+01 dihedral pdb=" CA ILE B 26 " pdb=" C ILE B 26 " pdb=" N ASN B 27 " pdb=" CA ASN B 27 " ideal model delta harmonic sigma weight residual 180.00 162.62 17.38 0 5.00e+00 4.00e-02 1.21e+01 dihedral pdb=" CA ILE A 26 " pdb=" C ILE A 26 " pdb=" N ASN A 27 " pdb=" CA ASN A 27 " ideal model delta harmonic sigma weight residual 180.00 162.63 17.37 0 5.00e+00 4.00e-02 1.21e+01 ... (remaining 1296 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 173 0.024 - 0.048: 90 0.048 - 0.072: 36 0.072 - 0.097: 24 0.097 - 0.121: 31 Chirality restraints: 354 Sorted by residual: chirality pdb=" CA VAL B 65 " pdb=" N VAL B 65 " pdb=" C VAL B 65 " pdb=" CB VAL B 65 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.64e-01 chirality pdb=" CA VAL B 121 " pdb=" N VAL B 121 " pdb=" C VAL B 121 " pdb=" CB VAL B 121 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.58e-01 chirality pdb=" CA VAL A 65 " pdb=" N VAL A 65 " pdb=" C VAL A 65 " pdb=" CB VAL A 65 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.50e-01 ... (remaining 351 not shown) Planarity restraints: 366 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 33 " -0.010 2.00e-02 2.50e+03 9.21e-03 1.48e+00 pdb=" CG PHE B 33 " 0.019 2.00e-02 2.50e+03 pdb=" CD1 PHE B 33 " 0.004 2.00e-02 2.50e+03 pdb=" CD2 PHE B 33 " -0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE B 33 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 PHE B 33 " 0.002 2.00e-02 2.50e+03 pdb=" CZ PHE B 33 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 33 " -0.010 2.00e-02 2.50e+03 9.16e-03 1.47e+00 pdb=" CG PHE A 33 " 0.019 2.00e-02 2.50e+03 pdb=" CD1 PHE A 33 " 0.005 2.00e-02 2.50e+03 pdb=" CD2 PHE A 33 " -0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE A 33 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 PHE A 33 " 0.002 2.00e-02 2.50e+03 pdb=" CZ PHE A 33 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 33 " -0.011 2.00e-02 2.50e+03 9.13e-03 1.46e+00 pdb=" CG PHE C 33 " 0.019 2.00e-02 2.50e+03 pdb=" CD1 PHE C 33 " 0.004 2.00e-02 2.50e+03 pdb=" CD2 PHE C 33 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE C 33 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 PHE C 33 " 0.002 2.00e-02 2.50e+03 pdb=" CZ PHE C 33 " -0.001 2.00e-02 2.50e+03 ... (remaining 363 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.85: 648 2.85 - 3.36: 1648 3.36 - 3.88: 3728 3.88 - 4.39: 3906 4.39 - 4.90: 7337 Nonbonded interactions: 17267 Sorted by model distance: nonbonded pdb=" OG1 THR B 119 " pdb=" OH TYR C 114 " model vdw 2.340 3.040 nonbonded pdb=" OH TYR B 114 " pdb=" OG1 THR A 119 " model vdw 2.359 3.040 nonbonded pdb=" OG SER B 115 " pdb=" O SER C 23 " model vdw 2.529 3.040 nonbonded pdb=" O SER B 23 " pdb=" OG SER A 115 " model vdw 2.552 3.040 nonbonded pdb=" OH TYR C 78 " pdb=" OG SER C 97 " model vdw 2.570 3.040 ... (remaining 17262 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: 0.00 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'A' selection = chain 'C' } 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: 0.510 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: 0.010 Extract box with map and model: 0.020 Check model and map are aligned: 0.000 Set scattering table: 0.020 Process input model: 3.470 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 2196 Z= 0.154 Angle : 0.693 5.327 2988 Z= 0.418 Chirality : 0.047 0.121 354 Planarity : 0.004 0.030 366 Dihedral : 17.078 88.669 777 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 0.00 % Allowed : 27.85 % Favored : 72.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.78 (0.46), residues: 261 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.35 (0.35), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 34 TYR 0.018 0.002 TYR A 114 PHE 0.019 0.003 PHE B 33 TRP 0.003 0.001 TRP C 79 HIS 0.003 0.001 HIS B 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.15 ( 2196) covalent geometry : angle 0.69290 / 0.42 ( 2988) hydrogen bonds : bond 0.18337 / 10.87 ( 41) hydrogen bonds : angle 10.57038 / 7.32 ( 123) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 522 Ramachandran restraints generated. 261 Oldfield, 0 Emsley, 261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 522 Ramachandran restraints generated. 261 Oldfield, 0 Emsley, 261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.054 Fit side-chains REVERT: A 62 GLU cc_start: 0.7951 (mt-10) cc_final: 0.7475 (pt0) outliers start: 0 outliers final: 0 residues processed: 58 average time/residue: 0.4528 time to fit residues: 26.6614 Evaluate side-chains 53 residues out of total 237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 0.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 12 optimal weight: 10.0000 chunk 24 optimal weight: 5.9990 chunk 13 optimal weight: 0.0050 chunk 1 optimal weight: 9.9990 chunk 8 optimal weight: 2.9990 chunk 16 optimal weight: 7.9990 chunk 15 optimal weight: 3.9990 chunk 25 optimal weight: 7.9990 chunk 26 optimal weight: 0.9980 chunk 9 optimal weight: 10.0000 chunk 11 optimal weight: 3.9990 overall best weight: 2.4000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 90 HIS ** A 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 90 HIS C 90 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.120812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.101547 restraints weight = 2445.909| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 1.83 r_work: 0.3297 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3198 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8664 moved from start: 0.2046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 2196 Z= 0.137 Angle : 0.549 4.674 2988 Z= 0.304 Chirality : 0.049 0.138 354 Planarity : 0.004 0.027 366 Dihedral : 5.567 22.681 294 Min Nonbonded Distance : 2.657 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 5.91 % Allowed : 23.21 % Favored : 70.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.96 (0.45), residues: 261 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.49 (0.34), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 34 TYR 0.013 0.002 TYR A 114 PHE 0.009 0.002 PHE A 33 TRP 0.002 0.001 TRP C 79 HIS 0.001 0.001 HIS B 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 ( 2196) covalent geometry : angle 0.54874 / 0.30 ( 2988) hydrogen bonds : bond 0.02940 / 1.74 ( 41) hydrogen bonds : angle 6.43780 / 4.39 ( 123) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 522 Ramachandran restraints generated. 261 Oldfield, 0 Emsley, 261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 522 Ramachandran restraints generated. 261 Oldfield, 0 Emsley, 261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 48 time to evaluate : 0.079 Fit side-chains REVERT: B 62 GLU cc_start: 0.7937 (mt-10) cc_final: 0.7377 (pt0) REVERT: B 82 LEU cc_start: 0.9004 (OUTLIER) cc_final: 0.8615 (mt) REVERT: A 34 ARG cc_start: 0.8108 (ttt-90) cc_final: 0.7791 (ttt90) REVERT: A 62 GLU cc_start: 0.7877 (mt-10) cc_final: 0.7351 (pt0) REVERT: A 104 ARG cc_start: 0.8592 (OUTLIER) cc_final: 0.8284 (mtt-85) REVERT: C 92 GLU cc_start: 0.8226 (mp0) cc_final: 0.7888 (mt-10) REVERT: C 104 ARG cc_start: 0.8400 (OUTLIER) cc_final: 0.8060 (mtt-85) outliers start: 14 outliers final: 2 residues processed: 58 average time/residue: 0.4921 time to fit residues: 29.0214 Evaluate side-chains 49 residues out of total 237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 44 time to evaluate : 0.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 MET Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 104 ARG Chi-restraints excluded: chain C residue 104 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 12 optimal weight: 0.0050 chunk 15 optimal weight: 10.0000 chunk 8 optimal weight: 9.9990 chunk 5 optimal weight: 10.0000 chunk 7 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 11 optimal weight: 7.9990 chunk 9 optimal weight: 9.9990 chunk 19 optimal weight: 4.9990 chunk 26 optimal weight: 0.1980 chunk 4 optimal weight: 9.9990 overall best weight: 2.6400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 98 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.118745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.099671 restraints weight = 2489.275| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 1.80 r_work: 0.3266 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3170 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8682 moved from start: 0.2236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 2196 Z= 0.143 Angle : 0.538 3.636 2988 Z= 0.299 Chirality : 0.049 0.138 354 Planarity : 0.004 0.027 366 Dihedral : 5.628 22.809 294 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 5.06 % Allowed : 23.21 % Favored : 71.73 % 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: -1.98 (0.45), residues: 261 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.50 (0.35), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 34 TYR 0.014 0.002 TYR A 114 PHE 0.010 0.002 PHE B 33 TRP 0.003 0.001 TRP C 79 HIS 0.003 0.001 HIS A 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.14 ( 2196) covalent geometry : angle 0.53816 / 0.30 ( 2988) hydrogen bonds : bond 0.02989 / 1.75 ( 41) hydrogen bonds : angle 5.99897 / 4.07 ( 123) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 522 Ramachandran restraints generated. 261 Oldfield, 0 Emsley, 261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 522 Ramachandran restraints generated. 261 Oldfield, 0 Emsley, 261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 48 time to evaluate : 0.081 Fit side-chains REVERT: B 82 LEU cc_start: 0.8978 (OUTLIER) cc_final: 0.8568 (mt) REVERT: A 34 ARG cc_start: 0.8151 (ttt-90) cc_final: 0.7793 (ttt90) REVERT: A 62 GLU cc_start: 0.7908 (mt-10) cc_final: 0.7408 (tt0) REVERT: A 80 LYS cc_start: 0.9001 (ttpp) cc_final: 0.8724 (tttp) REVERT: A 104 ARG cc_start: 0.8601 (OUTLIER) cc_final: 0.8281 (mtt-85) REVERT: C 92 GLU cc_start: 0.8283 (mp0) cc_final: 0.7921 (mt-10) REVERT: C 104 ARG cc_start: 0.8435 (OUTLIER) cc_final: 0.8097 (mtt-85) outliers start: 12 outliers final: 4 residues processed: 55 average time/residue: 0.6884 time to fit residues: 38.4243 Evaluate side-chains 54 residues out of total 237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 47 time to evaluate : 0.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 13 MET Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 104 ARG Chi-restraints excluded: chain C residue 104 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 25 optimal weight: 9.9990 chunk 12 optimal weight: 4.9990 chunk 24 optimal weight: 20.0000 chunk 3 optimal weight: 0.9990 chunk 8 optimal weight: 8.9990 chunk 17 optimal weight: 1.9990 chunk 11 optimal weight: 5.9990 chunk 1 optimal weight: 0.7980 chunk 20 optimal weight: 9.9990 chunk 10 optimal weight: 0.0980 chunk 7 optimal weight: 0.9980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.123422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.105011 restraints weight = 2456.201| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 1.79 r_work: 0.3377 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3281 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.2298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 2196 Z= 0.082 Angle : 0.468 3.338 2988 Z= 0.258 Chirality : 0.048 0.126 354 Planarity : 0.004 0.033 366 Dihedral : 5.110 21.120 294 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 4.22 % Allowed : 24.47 % Favored : 71.31 % 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: -1.94 (0.46), residues: 261 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.47 (0.35), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 34 TYR 0.011 0.001 TYR B 114 PHE 0.006 0.001 PHE B 64 TRP 0.002 0.001 TRP C 79 HIS 0.005 0.001 HIS B 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00193 / 0.08 ( 2196) covalent geometry : angle 0.46794 / 0.26 ( 2988) hydrogen bonds : bond 0.02085 / 1.20 ( 41) hydrogen bonds : angle 5.51113 / 3.73 ( 123) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 522 Ramachandran restraints generated. 261 Oldfield, 0 Emsley, 261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 522 Ramachandran restraints generated. 261 Oldfield, 0 Emsley, 261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 46 time to evaluate : 0.084 Fit side-chains REVERT: B 82 LEU cc_start: 0.8952 (OUTLIER) cc_final: 0.8625 (mt) REVERT: A 34 ARG cc_start: 0.8138 (ttt-90) cc_final: 0.7818 (ttt90) REVERT: A 62 GLU cc_start: 0.7868 (mt-10) cc_final: 0.7455 (tt0) REVERT: C 92 GLU cc_start: 0.8296 (mp0) cc_final: 0.7963 (mt-10) outliers start: 10 outliers final: 3 residues processed: 53 average time/residue: 0.6635 time to fit residues: 35.7672 Evaluate side-chains 50 residues out of total 237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 46 time to evaluate : 0.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 97 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 9 optimal weight: 9.9990 chunk 24 optimal weight: 20.0000 chunk 15 optimal weight: 4.9990 chunk 7 optimal weight: 1.9990 chunk 20 optimal weight: 8.9990 chunk 2 optimal weight: 6.9990 chunk 8 optimal weight: 6.9990 chunk 4 optimal weight: 10.0000 chunk 19 optimal weight: 1.9990 chunk 6 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 27 ASN ** 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 = 0.3619 r_free = 0.3619 target = 0.116322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.097239 restraints weight = 2523.747| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 1.78 r_work: 0.3235 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3137 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8718 moved from start: 0.2555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 2196 Z= 0.227 Angle : 0.616 5.003 2988 Z= 0.338 Chirality : 0.052 0.151 354 Planarity : 0.005 0.030 366 Dihedral : 5.962 23.781 294 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 5.49 % Allowed : 21.94 % Favored : 72.57 % 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: -1.98 (0.46), residues: 261 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.50 (0.35), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 34 TYR 0.018 0.002 TYR A 114 PHE 0.013 0.003 PHE B 33 TRP 0.004 0.001 TRP C 79 HIS 0.004 0.001 HIS A 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00539 / 0.23 ( 2196) covalent geometry : angle 0.61551 / 0.34 ( 2988) hydrogen bonds : bond 0.03225 / 1.92 ( 41) hydrogen bonds : angle 6.09088 / 4.09 ( 123) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 522 Ramachandran restraints generated. 261 Oldfield, 0 Emsley, 261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 522 Ramachandran restraints generated. 261 Oldfield, 0 Emsley, 261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 50 time to evaluate : 0.109 Fit side-chains REVERT: B 58 LEU cc_start: 0.7559 (OUTLIER) cc_final: 0.7050 (mp) REVERT: B 82 LEU cc_start: 0.8922 (OUTLIER) cc_final: 0.8438 (mp) REVERT: A 62 GLU cc_start: 0.7921 (mt-10) cc_final: 0.7418 (tt0) REVERT: A 80 LYS cc_start: 0.9016 (ttpp) cc_final: 0.8736 (tttp) REVERT: C 82 LEU cc_start: 0.8898 (OUTLIER) cc_final: 0.8407 (mp) REVERT: C 92 GLU cc_start: 0.8245 (mp0) cc_final: 0.7888 (mt-10) outliers start: 13 outliers final: 4 residues processed: 58 average time/residue: 0.7078 time to fit residues: 41.6575 Evaluate side-chains 57 residues out of total 237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 50 time to evaluate : 0.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 MET Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain C residue 82 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 13 optimal weight: 8.9990 chunk 19 optimal weight: 10.0000 chunk 10 optimal weight: 0.9980 chunk 15 optimal weight: 4.9990 chunk 22 optimal weight: 0.9980 chunk 9 optimal weight: 7.9990 chunk 1 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 23 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 chunk 3 optimal weight: 2.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 90 HIS ** C 27 ASN ** 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 = 0.3677 r_free = 0.3677 target = 0.120443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.101939 restraints weight = 2415.373| |-----------------------------------------------------------------------------| r_work (start): 0.3432 rms_B_bonded: 1.74 r_work: 0.3325 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3229 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 moved from start: 0.2545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 2196 Z= 0.099 Angle : 0.496 3.501 2988 Z= 0.272 Chirality : 0.048 0.128 354 Planarity : 0.003 0.024 366 Dihedral : 5.384 22.189 294 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 5.06 % Allowed : 23.21 % Favored : 71.73 % 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: -1.96 (0.46), residues: 261 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.48 (0.35), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 34 TYR 0.013 0.001 TYR B 114 PHE 0.008 0.002 PHE B 33 TRP 0.002 0.001 TRP C 79 HIS 0.005 0.001 HIS B 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.10 ( 2196) covalent geometry : angle 0.49598 / 0.27 ( 2988) hydrogen bonds : bond 0.02258 / 1.34 ( 41) hydrogen bonds : angle 5.62049 / 3.76 ( 123) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 522 Ramachandran restraints generated. 261 Oldfield, 0 Emsley, 261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 522 Ramachandran restraints generated. 261 Oldfield, 0 Emsley, 261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 47 time to evaluate : 0.070 Fit side-chains REVERT: B 58 LEU cc_start: 0.7625 (OUTLIER) cc_final: 0.7094 (mp) REVERT: B 82 LEU cc_start: 0.8934 (OUTLIER) cc_final: 0.8557 (mt) REVERT: A 21 ARG cc_start: 0.8132 (ttt180) cc_final: 0.7907 (ttt90) REVERT: A 34 ARG cc_start: 0.8181 (ttm-80) cc_final: 0.7842 (ttt90) REVERT: A 62 GLU cc_start: 0.7884 (mt-10) cc_final: 0.7452 (tt0) REVERT: C 92 GLU cc_start: 0.8235 (mp0) cc_final: 0.7900 (mt-10) REVERT: C 104 ARG cc_start: 0.8381 (OUTLIER) cc_final: 0.8047 (mtt-85) outliers start: 12 outliers final: 3 residues processed: 53 average time/residue: 0.7369 time to fit residues: 39.6041 Evaluate side-chains 53 residues out of total 237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 47 time to evaluate : 0.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain C residue 104 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 14 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 4 optimal weight: 10.0000 chunk 24 optimal weight: 20.0000 chunk 1 optimal weight: 9.9990 chunk 5 optimal weight: 4.9990 chunk 7 optimal weight: 3.9990 chunk 15 optimal weight: 4.9990 chunk 3 optimal weight: 5.9990 chunk 21 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 31 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 = 0.3615 r_free = 0.3615 target = 0.115957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.097095 restraints weight = 2489.481| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 1.76 r_work: 0.3237 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3140 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8722 moved from start: 0.2681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 2196 Z= 0.210 Angle : 0.604 3.908 2988 Z= 0.331 Chirality : 0.051 0.140 354 Planarity : 0.005 0.036 366 Dihedral : 5.931 23.667 294 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 5.06 % Allowed : 23.63 % Favored : 71.31 % 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: -1.96 (0.46), residues: 261 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.48 (0.35), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 34 TYR 0.019 0.002 TYR A 114 PHE 0.014 0.003 PHE B 33 TRP 0.004 0.001 TRP C 79 HIS 0.005 0.001 HIS B 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00497 / 0.21 ( 2196) covalent geometry : angle 0.60395 / 0.33 ( 2988) hydrogen bonds : bond 0.02999 / 1.80 ( 41) hydrogen bonds : angle 6.07802 / 4.05 ( 123) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 522 Ramachandran restraints generated. 261 Oldfield, 0 Emsley, 261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 522 Ramachandran restraints generated. 261 Oldfield, 0 Emsley, 261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 49 time to evaluate : 0.073 Fit side-chains REVERT: B 58 LEU cc_start: 0.7593 (OUTLIER) cc_final: 0.7076 (mp) REVERT: B 82 LEU cc_start: 0.8927 (OUTLIER) cc_final: 0.8445 (mp) REVERT: A 34 ARG cc_start: 0.8222 (ttm-80) cc_final: 0.7885 (ttt90) REVERT: A 62 GLU cc_start: 0.7938 (mt-10) cc_final: 0.7443 (tt0) REVERT: A 80 LYS cc_start: 0.8988 (ttpp) cc_final: 0.8708 (tttp) REVERT: C 62 GLU cc_start: 0.8123 (mt-10) cc_final: 0.7781 (mt-10) REVERT: C 92 GLU cc_start: 0.8252 (mp0) cc_final: 0.7912 (mt-10) REVERT: C 104 ARG cc_start: 0.8453 (OUTLIER) cc_final: 0.8116 (mtt-85) outliers start: 12 outliers final: 5 residues processed: 55 average time/residue: 0.6924 time to fit residues: 38.6315 Evaluate side-chains 57 residues out of total 237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 49 time to evaluate : 0.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 MET Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain C residue 97 SER Chi-restraints excluded: chain C residue 104 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 7 optimal weight: 1.9990 chunk 19 optimal weight: 6.9990 chunk 2 optimal weight: 20.0000 chunk 6 optimal weight: 6.9990 chunk 10 optimal weight: 9.9990 chunk 8 optimal weight: 4.9990 chunk 25 optimal weight: 3.9990 chunk 0 optimal weight: 9.9990 chunk 15 optimal weight: 4.9990 chunk 13 optimal weight: 6.9990 chunk 16 optimal weight: 2.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 90 HIS ** C 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 31 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 = 0.3607 r_free = 0.3607 target = 0.115784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.096903 restraints weight = 2475.652| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 1.76 r_work: 0.3238 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3141 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8720 moved from start: 0.2704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.028 2196 Z= 0.193 Angle : 0.598 5.202 2988 Z= 0.325 Chirality : 0.051 0.140 354 Planarity : 0.004 0.034 366 Dihedral : 5.954 23.469 294 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 5.49 % Allowed : 24.05 % Favored : 70.46 % 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: -1.97 (0.46), residues: 261 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.49 (0.35), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 34 TYR 0.017 0.002 TYR A 114 PHE 0.014 0.003 PHE B 33 TRP 0.003 0.001 TRP C 79 HIS 0.005 0.001 HIS B 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00457 / 0.19 ( 2196) covalent geometry : angle 0.59846 / 0.33 ( 2988) hydrogen bonds : bond 0.02919 / 1.74 ( 41) hydrogen bonds : angle 6.04181 / 4.02 ( 123) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 522 Ramachandran restraints generated. 261 Oldfield, 0 Emsley, 261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 522 Ramachandran restraints generated. 261 Oldfield, 0 Emsley, 261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 50 time to evaluate : 0.050 Fit side-chains REVERT: B 34 ARG cc_start: 0.7976 (OUTLIER) cc_final: 0.7753 (ttt-90) REVERT: B 58 LEU cc_start: 0.7609 (OUTLIER) cc_final: 0.7119 (mp) REVERT: B 82 LEU cc_start: 0.8936 (OUTLIER) cc_final: 0.8468 (mp) REVERT: A 34 ARG cc_start: 0.8218 (ttm-80) cc_final: 0.7877 (ttt90) REVERT: A 62 GLU cc_start: 0.7961 (mt-10) cc_final: 0.7464 (tt0) REVERT: A 80 LYS cc_start: 0.8991 (ttpp) cc_final: 0.8714 (tttp) REVERT: C 13 MET cc_start: 0.8255 (OUTLIER) cc_final: 0.7312 (mpp) REVERT: C 62 GLU cc_start: 0.8065 (mt-10) cc_final: 0.7707 (mt-10) REVERT: C 92 GLU cc_start: 0.8264 (mp0) cc_final: 0.7925 (mt-10) REVERT: C 104 ARG cc_start: 0.8454 (OUTLIER) cc_final: 0.8110 (mtt-85) outliers start: 13 outliers final: 3 residues processed: 57 average time/residue: 0.5036 time to fit residues: 29.1146 Evaluate side-chains 58 residues out of total 237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 50 time to evaluate : 0.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 34 ARG Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain C residue 13 MET Chi-restraints excluded: chain C residue 104 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 25 optimal weight: 8.9990 chunk 8 optimal weight: 6.9990 chunk 18 optimal weight: 9.9990 chunk 17 optimal weight: 1.9990 chunk 10 optimal weight: 9.9990 chunk 3 optimal weight: 8.9990 chunk 24 optimal weight: 10.0000 chunk 7 optimal weight: 0.6980 chunk 22 optimal weight: 3.9990 chunk 14 optimal weight: 6.9990 chunk 20 optimal weight: 5.9990 overall best weight: 3.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 90 HIS ** C 27 ASN ** 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 = 0.3609 r_free = 0.3609 target = 0.115758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.096798 restraints weight = 2458.921| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 1.75 r_work: 0.3239 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3142 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8721 moved from start: 0.2746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 2196 Z= 0.200 Angle : 0.609 4.513 2988 Z= 0.331 Chirality : 0.051 0.148 354 Planarity : 0.005 0.038 366 Dihedral : 5.980 23.536 294 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 5.06 % Allowed : 24.47 % Favored : 70.46 % 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: -2.00 (0.46), residues: 261 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.52 (0.35), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 34 TYR 0.018 0.002 TYR C 114 PHE 0.014 0.003 PHE B 33 TRP 0.003 0.001 TRP C 79 HIS 0.004 0.001 HIS B 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00473 / 0.20 ( 2196) covalent geometry : angle 0.60914 / 0.33 ( 2988) hydrogen bonds : bond 0.02943 / 1.75 ( 41) hydrogen bonds : angle 6.01671 / 4.01 ( 123) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 522 Ramachandran restraints generated. 261 Oldfield, 0 Emsley, 261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 522 Ramachandran restraints generated. 261 Oldfield, 0 Emsley, 261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 51 time to evaluate : 0.057 Fit side-chains REVERT: B 34 ARG cc_start: 0.7979 (OUTLIER) cc_final: 0.7751 (ttt-90) REVERT: B 58 LEU cc_start: 0.7598 (OUTLIER) cc_final: 0.7108 (mp) REVERT: B 82 LEU cc_start: 0.8916 (OUTLIER) cc_final: 0.8432 (mp) REVERT: A 34 ARG cc_start: 0.8225 (ttm-80) cc_final: 0.7886 (ttt90) REVERT: A 62 GLU cc_start: 0.7967 (mt-10) cc_final: 0.7460 (tt0) REVERT: A 80 LYS cc_start: 0.8993 (ttpp) cc_final: 0.8720 (tttp) REVERT: C 62 GLU cc_start: 0.8074 (mt-10) cc_final: 0.7708 (mt-10) REVERT: C 92 GLU cc_start: 0.8244 (mp0) cc_final: 0.7905 (mt-10) REVERT: C 104 ARG cc_start: 0.8459 (OUTLIER) cc_final: 0.8114 (mtt-85) outliers start: 12 outliers final: 5 residues processed: 57 average time/residue: 0.6163 time to fit residues: 35.5831 Evaluate side-chains 60 residues out of total 237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 51 time to evaluate : 0.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 MET Chi-restraints excluded: chain B residue 34 ARG Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain C residue 97 SER Chi-restraints excluded: chain C residue 104 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 24 optimal weight: 20.0000 chunk 3 optimal weight: 10.0000 chunk 12 optimal weight: 5.9990 chunk 10 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 25 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 9 optimal weight: 7.9990 chunk 5 optimal weight: 7.9990 chunk 1 optimal weight: 1.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 90 HIS ** C 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 31 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 = 0.3611 r_free = 0.3611 target = 0.115908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.097018 restraints weight = 2531.539| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 1.78 r_work: 0.3242 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3144 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8718 moved from start: 0.2725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 2196 Z= 0.178 Angle : 0.592 4.700 2988 Z= 0.321 Chirality : 0.050 0.134 354 Planarity : 0.004 0.039 366 Dihedral : 5.934 23.399 294 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 3.38 % Allowed : 26.58 % Favored : 70.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.98 (0.46), residues: 261 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.50 (0.35), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 34 TYR 0.017 0.002 TYR C 114 PHE 0.013 0.003 PHE B 33 TRP 0.003 0.001 TRP C 79 HIS 0.006 0.001 HIS B 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00420 / 0.18 ( 2196) covalent geometry : angle 0.59184 / 0.32 ( 2988) hydrogen bonds : bond 0.02799 / 1.66 ( 41) hydrogen bonds : angle 5.95638 / 3.98 ( 123) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 522 Ramachandran restraints generated. 261 Oldfield, 0 Emsley, 261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 522 Ramachandran restraints generated. 261 Oldfield, 0 Emsley, 261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 51 time to evaluate : 0.083 Fit side-chains REVERT: B 58 LEU cc_start: 0.7608 (OUTLIER) cc_final: 0.7122 (mp) REVERT: B 82 LEU cc_start: 0.8915 (OUTLIER) cc_final: 0.8456 (mp) REVERT: A 34 ARG cc_start: 0.8239 (ttm-80) cc_final: 0.7895 (ttt90) REVERT: A 62 GLU cc_start: 0.7965 (mt-10) cc_final: 0.7507 (tt0) REVERT: A 80 LYS cc_start: 0.8990 (ttpp) cc_final: 0.8714 (tttp) REVERT: C 62 GLU cc_start: 0.8071 (mt-10) cc_final: 0.7707 (mt-10) REVERT: C 92 GLU cc_start: 0.8266 (mp0) cc_final: 0.7920 (mt-10) REVERT: C 104 ARG cc_start: 0.8465 (OUTLIER) cc_final: 0.8127 (mtt-85) outliers start: 8 outliers final: 4 residues processed: 55 average time/residue: 0.6634 time to fit residues: 37.0213 Evaluate side-chains 57 residues out of total 237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 50 time to evaluate : 0.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 MET Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain C residue 104 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 1 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 11 optimal weight: 9.9990 chunk 6 optimal weight: 10.0000 chunk 17 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 24 optimal weight: 9.9990 chunk 16 optimal weight: 3.9990 chunk 14 optimal weight: 9.9990 chunk 8 optimal weight: 0.7980 chunk 21 optimal weight: 4.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 90 HIS ** C 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 31 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 = 0.3623 r_free = 0.3623 target = 0.116886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.098031 restraints weight = 2489.736| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 1.76 r_work: 0.3256 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3158 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8704 moved from start: 0.2726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 2196 Z= 0.151 Angle : 0.569 4.774 2988 Z= 0.308 Chirality : 0.050 0.132 354 Planarity : 0.004 0.039 366 Dihedral : 5.769 23.144 294 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 4.22 % Allowed : 24.89 % Favored : 70.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.99 (0.46), residues: 261 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.51 (0.35), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 34 TYR 0.015 0.002 TYR A 114 PHE 0.011 0.002 PHE B 33 TRP 0.003 0.001 TRP C 79 HIS 0.006 0.001 HIS B 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.15 ( 2196) covalent geometry : angle 0.56906 / 0.31 ( 2988) hydrogen bonds : bond 0.02635 / 1.56 ( 41) hydrogen bonds : angle 5.86105 / 3.90 ( 123) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1092.90 seconds wall clock time: 19 minutes 17.21 seconds (1157.21 seconds total)