Starting phenix.real_space_refine on Tue Aug 4 12:03:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9wa2_65797/08_2026/9wa2_65797.cif Found real_map, /net/cci-nas-00/data/ceres_data/9wa2_65797/08_2026/9wa2_65797.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9wa2_65797/08_2026/9wa2_65797.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9wa2_65797/08_2026/9wa2_65797.map" model { file = "/net/cci-nas-00/data/ceres_data/9wa2_65797/08_2026/9wa2_65797.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9wa2_65797/08_2026/9wa2_65797.cif" } resolution = 2.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 3 5.16 5 C 1389 2.51 5 N 357 2.21 5 O 405 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: 2154 Number of models: 1 Model: "" Number of chains: 1 Chain: "B" Number of atoms: 718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 718 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain breaks: 1 Restraints were copied for chains: A, C Time building chain proxies: 0.44, per 1000 atoms: 0.20 Number of scatterers: 2154 At special positions: 0 Unit cell: (73.47, 84.63, 31.62, 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 405 8.00 N 357 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: 0.09 Conformation dependent library (CDL) restraints added in 49.2 milliseconds 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 528 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 10 sheets defined 0.0% alpha, 44.6% 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 12 through 16 Processing sheet with id=AA2, first strand: chain 'A' and resid 19 through 21 removed outlier: 6.624A 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: 6.347A pdb=" N ALA B 25 " --> pdb=" O ILE C 26 " (cutoff:3.500A) removed outlier: 7.760A pdb=" N VAL C 28 " --> pdb=" O ALA B 25 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N ASN B 27 " --> pdb=" O VAL C 28 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N VAL C 30 " --> pdb=" O ASN B 27 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N ALA B 29 " --> pdb=" O VAL C 30 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N VAL C 32 " --> pdb=" O ALA B 29 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N HIS B 31 " --> pdb=" O VAL C 32 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N ARG C 34 " --> pdb=" O HIS B 31 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N VAL B 33 " --> pdb=" O ARG C 34 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 59 through 60 removed outlier: 6.282A pdb=" N THR B 59 " --> pdb=" O THR A 60 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 64 through 65 removed outlier: 6.758A pdb=" N PHE B 64 " --> pdb=" O VAL A 65 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 69 through 75 removed outlier: 6.556A pdb=" N LYS B 70 " --> pdb=" O VAL A 71 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N ILE A 73 " --> pdb=" O LYS B 70 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N GLU B 72 " --> pdb=" O ILE A 73 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N THR A 75 " --> pdb=" O GLU B 72 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N ASP B 74 " --> pdb=" O THR A 75 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N THR B 75 " --> pdb=" O ASP C 74 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 92 through 98 removed outlier: 6.712A pdb=" N VAL B 93 " --> pdb=" O VAL C 94 " (cutoff:3.500A) removed outlier: 7.942A pdb=" N THR C 96 " --> pdb=" O VAL B 93 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N PHE B 95 " --> pdb=" O THR C 96 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N ASN C 98 " --> pdb=" O PHE B 95 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N ALA B 97 " --> pdb=" O ASN C 98 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 103 through 110 removed outlier: 8.938A pdb=" N ARG B 103 " --> pdb=" O ARG A 104 " (cutoff:3.500A) removed outlier: 9.967A pdb=" N THR A 106 " --> pdb=" O ARG B 103 " (cutoff:3.500A) removed outlier: 9.188A pdb=" N TYR B 105 " --> pdb=" O THR A 106 " (cutoff:3.500A) removed outlier: 9.984A pdb=" N ALA A 108 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ILE B 107 " --> pdb=" O ALA A 108 " (cutoff:3.500A) removed outlier: 8.121A pdb=" N LEU A 110 " --> pdb=" O ILE B 107 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N ALA B 109 " --> pdb=" O LEU A 110 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N ARG B 104 " --> pdb=" O ARG C 103 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N TYR C 105 " --> pdb=" O ARG B 104 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N THR B 106 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N ILE C 107 " --> pdb=" O THR B 106 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N ALA B 108 " --> pdb=" O ILE C 107 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 114 through 115 removed outlier: 6.787A pdb=" N TYR B 114 " --> pdb=" O SER A 115 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 118 through 122 removed outlier: 5.782A pdb=" N THR B 118 " --> pdb=" O THR C 119 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N VAL C 121 " --> pdb=" O THR B 118 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N ALA B 120 " --> pdb=" O VAL C 121 " (cutoff:3.500A) 39 hydrogen bonds defined for protein. 117 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: 0.16 Time building geometry restraints manager: 0.13 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: 564 1.33 - 1.45: 387 1.45 - 1.57: 1245 1.57 - 1.68: 0 1.68 - 1.80: 6 Bond restraints: 2202 Sorted by residual: bond pdb=" C VAL B 122 " pdb=" O VAL B 122 " ideal model delta sigma weight residual 1.236 1.214 0.022 1.02e-02 9.61e+03 4.86e+00 bond pdb=" C VAL C 122 " pdb=" O VAL C 122 " ideal model delta sigma weight residual 1.236 1.214 0.022 1.02e-02 9.61e+03 4.84e+00 bond pdb=" C VAL A 122 " pdb=" O VAL A 122 " ideal model delta sigma weight residual 1.236 1.214 0.022 1.02e-02 9.61e+03 4.71e+00 bond pdb=" CA VAL A 122 " pdb=" C VAL A 122 " ideal model delta sigma weight residual 1.522 1.498 0.024 1.18e-02 7.18e+03 3.99e+00 bond pdb=" CA VAL B 122 " pdb=" C VAL B 122 " ideal model delta sigma weight residual 1.522 1.499 0.023 1.18e-02 7.18e+03 3.91e+00 ... (remaining 2197 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.40: 2747 1.40 - 2.80: 189 2.80 - 4.20: 46 4.20 - 5.60: 9 5.60 - 7.00: 9 Bond angle restraints: 3000 Sorted by residual: angle pdb=" CG ARG C 21 " pdb=" CD ARG C 21 " pdb=" NE ARG C 21 " ideal model delta sigma weight residual 112.00 119.00 -7.00 2.20e+00 2.07e-01 1.01e+01 angle pdb=" CG ARG A 21 " pdb=" CD ARG A 21 " pdb=" NE ARG A 21 " ideal model delta sigma weight residual 112.00 118.97 -6.97 2.20e+00 2.07e-01 1.00e+01 angle pdb=" CG ARG B 21 " pdb=" CD ARG B 21 " pdb=" NE ARG B 21 " ideal model delta sigma weight residual 112.00 118.94 -6.94 2.20e+00 2.07e-01 9.95e+00 angle pdb=" N THR C 123 " pdb=" CA THR C 123 " pdb=" C THR C 123 " ideal model delta sigma weight residual 112.41 116.51 -4.10 1.30e+00 5.92e-01 9.93e+00 angle pdb=" N THR B 123 " pdb=" CA THR B 123 " pdb=" C THR B 123 " ideal model delta sigma weight residual 112.41 116.49 -4.08 1.30e+00 5.92e-01 9.84e+00 ... (remaining 2995 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.66: 1155 13.66 - 27.32: 87 27.32 - 40.97: 54 40.97 - 54.63: 0 54.63 - 68.29: 12 Dihedral angle restraints: 1308 sinusoidal: 495 harmonic: 813 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 180.00 160.01 19.99 0 5.00e+00 4.00e-02 1.60e+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 180.00 160.02 19.98 0 5.00e+00 4.00e-02 1.60e+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 180.00 160.03 19.97 0 5.00e+00 4.00e-02 1.60e+01 ... (remaining 1305 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 147 0.024 - 0.047: 92 0.047 - 0.070: 59 0.070 - 0.094: 22 0.094 - 0.117: 40 Chirality restraints: 360 Sorted by residual: chirality pdb=" CA ILE B 107 " pdb=" N ILE B 107 " pdb=" C ILE B 107 " pdb=" CB ILE B 107 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.44e-01 chirality pdb=" CA ILE C 107 " pdb=" N ILE C 107 " pdb=" C ILE C 107 " pdb=" CB ILE C 107 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.42e-01 chirality pdb=" CA VAL C 14 " pdb=" N VAL C 14 " pdb=" C VAL C 14 " pdb=" CB VAL C 14 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.40e-01 ... (remaining 357 not shown) Planarity restraints: 369 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 104 " -0.180 9.50e-02 1.11e+02 8.13e-02 5.06e+00 pdb=" NE ARG B 104 " 0.017 2.00e-02 2.50e+03 pdb=" CZ ARG B 104 " -0.016 2.00e-02 2.50e+03 pdb=" NH1 ARG B 104 " 0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG B 104 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 104 " -0.179 9.50e-02 1.11e+02 8.09e-02 5.04e+00 pdb=" NE ARG A 104 " 0.017 2.00e-02 2.50e+03 pdb=" CZ ARG A 104 " -0.016 2.00e-02 2.50e+03 pdb=" NH1 ARG A 104 " 0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG A 104 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 104 " -0.179 9.50e-02 1.11e+02 8.08e-02 5.02e+00 pdb=" NE ARG C 104 " 0.017 2.00e-02 2.50e+03 pdb=" CZ ARG C 104 " -0.016 2.00e-02 2.50e+03 pdb=" NH1 ARG C 104 " 0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG C 104 " -0.001 2.00e-02 2.50e+03 ... (remaining 366 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 510 2.82 - 3.34: 1691 3.34 - 3.86: 3671 3.86 - 4.38: 3911 4.38 - 4.90: 7525 Nonbonded interactions: 17308 Sorted by model distance: nonbonded pdb=" NZ LYS B 76 " pdb=" OD1 ASP C 74 " model vdw 2.299 3.120 nonbonded pdb=" OD1 ASP B 74 " pdb=" NZ LYS A 76 " model vdw 2.318 3.120 nonbonded pdb=" O THR C 123 " pdb=" CG2 THR C 123 " model vdw 2.340 3.460 nonbonded pdb=" O THR A 123 " pdb=" CG2 THR A 123 " model vdw 2.341 3.460 nonbonded pdb=" O THR B 123 " pdb=" CG2 THR B 123 " model vdw 2.341 3.460 ... (remaining 17303 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: 0.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.030 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 2.520 Find NCS groups from input model: 0.010 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:4.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8695 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 : 0.004 0.024 2202 Z= 0.246 Angle : 0.907 6.998 3000 Z= 0.512 Chirality : 0.050 0.117 360 Planarity : 0.012 0.081 369 Dihedral : 14.296 68.287 780 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 0.00 % Allowed : 13.92 % Favored : 86.08 % 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: -2.40 (0.48), residues: 264 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.82 (0.36), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.005 ARG A 104 TYR 0.018 0.002 TYR A 114 PHE 0.011 0.002 PHE C 64 TRP 0.002 0.001 TRP A 79 HIS 0.004 0.001 HIS C 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00422 / 0.25 ( 2202) covalent geometry : angle 0.90662 / 0.51 ( 3000) hydrogen bonds : bond 0.14294 / 10.41 ( 39) hydrogen bonds : angle 9.08601 / 6.44 ( 117) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** 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 : 0.051 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 35 LYS cc_start: 0.8373 (ttpt) cc_final: 0.8097 (tttt) REVERT: C 59 THR cc_start: 0.8395 (m) cc_final: 0.7945 (p) outliers start: 0 outliers final: 0 residues processed: 53 average time/residue: 0.5349 time to fit residues: 28.7271 Evaluate side-chains 49 residues out of total 237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 0.054 ------------------------------------------------------------------------------- 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: 6.9990 chunk 13 optimal weight: 2.9990 chunk 1 optimal weight: 6.9990 chunk 8 optimal weight: 9.9990 chunk 16 optimal weight: 0.7980 chunk 15 optimal weight: 5.9990 chunk 25 optimal weight: 0.8980 chunk 26 optimal weight: 0.8980 chunk 9 optimal weight: 10.0000 chunk 11 optimal weight: 8.9990 overall best weight: 2.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 124 ASN C 31 HIS C 124 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.124633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.104951 restraints weight = 2481.417| |-----------------------------------------------------------------------------| r_work (start): 0.3541 rms_B_bonded: 1.92 r_work: 0.3432 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3340 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8748 moved from start: 0.1560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 2202 Z= 0.146 Angle : 0.550 3.528 3000 Z= 0.308 Chirality : 0.050 0.119 360 Planarity : 0.005 0.038 369 Dihedral : 5.503 20.381 297 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 1.27 % Allowed : 18.57 % Favored : 80.17 % 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: -2.20 (0.48), residues: 264 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.67 (0.37), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 104 TYR 0.016 0.002 TYR C 114 PHE 0.008 0.001 PHE B 95 TRP 0.002 0.001 TRP C 79 HIS 0.002 0.001 HIS B 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.15 ( 2202) covalent geometry : angle 0.54979 / 0.31 ( 3000) hydrogen bonds : bond 0.03032 / 2.30 ( 39) hydrogen bonds : angle 5.89476 / 4.13 ( 117) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 50 time to evaluate : 0.081 Fit side-chains revert: symmetry clash REVERT: B 59 THR cc_start: 0.8417 (m) cc_final: 0.8012 (p) REVERT: C 59 THR cc_start: 0.8494 (m) cc_final: 0.8008 (p) outliers start: 3 outliers final: 1 residues processed: 53 average time/residue: 0.5589 time to fit residues: 30.0533 Evaluate side-chains 49 residues out of total 237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 48 time to evaluate : 0.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 19 optimal weight: 3.9990 chunk 26 optimal weight: 0.9990 chunk 4 optimal weight: 9.9990 chunk 14 optimal weight: 7.9990 chunk 2 optimal weight: 10.0000 chunk 15 optimal weight: 9.9990 chunk 12 optimal weight: 0.8980 chunk 18 optimal weight: 9.9990 chunk 13 optimal weight: 0.9980 chunk 17 optimal weight: 9.9990 chunk 8 optimal weight: 1.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 124 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.125780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.105957 restraints weight = 2524.862| |-----------------------------------------------------------------------------| r_work (start): 0.3559 rms_B_bonded: 1.94 r_work: 0.3450 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3359 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8731 moved from start: 0.1810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 2202 Z= 0.124 Angle : 0.509 3.557 3000 Z= 0.284 Chirality : 0.049 0.130 360 Planarity : 0.004 0.030 369 Dihedral : 5.244 19.912 297 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 1.27 % Allowed : 17.30 % Favored : 81.43 % 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: -2.22 (0.49), residues: 264 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.68 (0.37), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 34 TYR 0.014 0.001 TYR C 114 PHE 0.009 0.001 PHE B 95 TRP 0.002 0.000 TRP C 79 HIS 0.002 0.001 HIS C 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.12 ( 2202) covalent geometry : angle 0.50949 / 0.28 ( 3000) hydrogen bonds : bond 0.02583 / 1.98 ( 39) hydrogen bonds : angle 5.37136 / 3.76 ( 117) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 48 time to evaluate : 0.050 Fit side-chains REVERT: B 59 THR cc_start: 0.8398 (m) cc_final: 0.7929 (p) REVERT: C 59 THR cc_start: 0.8510 (m) cc_final: 0.8007 (p) outliers start: 3 outliers final: 1 residues processed: 50 average time/residue: 0.6112 time to fit residues: 30.9698 Evaluate side-chains 49 residues out of total 237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 48 time to evaluate : 0.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 8 optimal weight: 10.0000 chunk 23 optimal weight: 0.0570 chunk 2 optimal weight: 10.0000 chunk 10 optimal weight: 9.9990 chunk 20 optimal weight: 3.9990 chunk 13 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 24 optimal weight: 5.9990 chunk 21 optimal weight: 6.9990 chunk 7 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 overall best weight: 2.6106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 124 ASN C 124 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.123172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.103355 restraints weight = 2482.653| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 1.91 r_work: 0.3408 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3318 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8757 moved from start: 0.1881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 2202 Z= 0.158 Angle : 0.529 3.600 3000 Z= 0.298 Chirality : 0.050 0.138 360 Planarity : 0.004 0.033 369 Dihedral : 5.338 20.653 297 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 1.69 % Allowed : 18.14 % Favored : 80.17 % 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: -2.26 (0.48), residues: 264 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.72 (0.37), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 34 TYR 0.014 0.002 TYR B 114 PHE 0.010 0.002 PHE B 95 TRP 0.002 0.001 TRP A 79 HIS 0.002 0.001 HIS A 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.16 ( 2202) covalent geometry : angle 0.52860 / 0.30 ( 3000) hydrogen bonds : bond 0.02575 / 1.96 ( 39) hydrogen bonds : angle 5.30220 / 3.69 ( 117) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 51 time to evaluate : 0.082 Fit side-chains REVERT: B 59 THR cc_start: 0.8532 (m) cc_final: 0.8051 (p) outliers start: 4 outliers final: 3 residues processed: 53 average time/residue: 0.8033 time to fit residues: 43.1090 Evaluate side-chains 55 residues out of total 237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 52 time to evaluate : 0.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LYS Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain C residue 66 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 16 optimal weight: 8.9990 chunk 12 optimal weight: 4.9990 chunk 11 optimal weight: 9.9990 chunk 2 optimal weight: 8.9990 chunk 10 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 21 optimal weight: 8.9990 chunk 14 optimal weight: 10.0000 chunk 23 optimal weight: 0.0980 chunk 7 optimal weight: 6.9990 chunk 8 optimal weight: 0.0970 overall best weight: 3.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 124 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.121555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.101830 restraints weight = 2506.375| |-----------------------------------------------------------------------------| r_work (start): 0.3494 rms_B_bonded: 1.91 r_work: 0.3382 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3291 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8776 moved from start: 0.2005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 2202 Z= 0.203 Angle : 0.565 3.690 3000 Z= 0.320 Chirality : 0.051 0.143 360 Planarity : 0.004 0.041 369 Dihedral : 5.515 21.292 297 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 2.11 % Allowed : 18.14 % Favored : 79.75 % 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: -2.33 (0.48), residues: 264 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.76 (0.36), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 34 TYR 0.015 0.002 TYR B 114 PHE 0.010 0.002 PHE B 95 TRP 0.002 0.001 TRP A 79 HIS 0.003 0.001 HIS A 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00472 / 0.20 ( 2202) covalent geometry : angle 0.56479 / 0.32 ( 3000) hydrogen bonds : bond 0.02755 / 2.07 ( 39) hydrogen bonds : angle 5.41564 / 3.77 ( 117) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 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: 5 poor density : 54 time to evaluate : 0.075 Fit side-chains revert: symmetry clash REVERT: A 72 GLU cc_start: 0.8785 (mt-10) cc_final: 0.8449 (mt-10) outliers start: 5 outliers final: 4 residues processed: 56 average time/residue: 0.7035 time to fit residues: 39.9469 Evaluate side-chains 57 residues out of total 237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 53 time to evaluate : 0.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LYS Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain C residue 66 GLU Chi-restraints excluded: chain C residue 92 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 22 optimal weight: 7.9990 chunk 6 optimal weight: 9.9990 chunk 11 optimal weight: 9.9990 chunk 23 optimal weight: 7.9990 chunk 5 optimal weight: 8.9990 chunk 9 optimal weight: 0.6980 chunk 25 optimal weight: 0.9990 chunk 1 optimal weight: 0.9990 chunk 17 optimal weight: 6.9990 chunk 13 optimal weight: 6.9990 chunk 10 optimal weight: 0.9980 overall best weight: 2.1386 ------------------------------------------------------------------------------- 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 = 0.3805 r_free = 0.3805 target = 0.123899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.104485 restraints weight = 2450.047| |-----------------------------------------------------------------------------| r_work (start): 0.3539 rms_B_bonded: 1.88 r_work: 0.3429 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3338 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8745 moved from start: 0.2060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2202 Z= 0.140 Angle : 0.516 3.580 3000 Z= 0.290 Chirality : 0.049 0.118 360 Planarity : 0.004 0.033 369 Dihedral : 5.291 20.452 297 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 1.69 % Allowed : 17.72 % Favored : 80.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.26 (0.48), residues: 264 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.72 (0.37), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 34 TYR 0.013 0.001 TYR B 114 PHE 0.008 0.001 PHE B 95 TRP 0.001 0.000 TRP C 79 HIS 0.002 0.001 HIS A 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 ( 2202) covalent geometry : angle 0.51618 / 0.29 ( 3000) hydrogen bonds : bond 0.02376 / 1.81 ( 39) hydrogen bonds : angle 5.16567 / 3.61 ( 117) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 50 time to evaluate : 0.084 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 53 average time/residue: 0.7539 time to fit residues: 40.4590 Evaluate side-chains 52 residues out of total 237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 50 time to evaluate : 0.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain C residue 66 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 11 optimal weight: 10.0000 chunk 14 optimal weight: 9.9990 chunk 21 optimal weight: 8.9990 chunk 15 optimal weight: 9.9990 chunk 1 optimal weight: 5.9990 chunk 8 optimal weight: 8.9990 chunk 18 optimal weight: 9.9990 chunk 6 optimal weight: 8.9990 chunk 5 optimal weight: 3.9990 chunk 19 optimal weight: 0.0470 chunk 26 optimal weight: 0.9980 overall best weight: 4.0084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 124 ASN C 124 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.120981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.101340 restraints weight = 2487.657| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 1.90 r_work: 0.3376 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3286 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8779 moved from start: 0.2100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 2202 Z= 0.219 Angle : 0.575 3.699 3000 Z= 0.326 Chirality : 0.050 0.120 360 Planarity : 0.005 0.043 369 Dihedral : 5.555 21.329 297 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 1.27 % Allowed : 18.99 % Favored : 79.75 % 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: -2.28 (0.48), residues: 264 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.73 (0.37), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 104 TYR 0.015 0.002 TYR B 114 PHE 0.011 0.002 PHE B 95 TRP 0.002 0.001 TRP A 79 HIS 0.003 0.001 HIS A 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00511 / 0.22 ( 2202) covalent geometry : angle 0.57515 / 0.33 ( 3000) hydrogen bonds : bond 0.02723 / 2.04 ( 39) hydrogen bonds : angle 5.38857 / 3.74 ( 117) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 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: 3 poor density : 53 time to evaluate : 0.083 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 72 GLU cc_start: 0.8755 (mt-10) cc_final: 0.8430 (mt-10) outliers start: 3 outliers final: 3 residues processed: 54 average time/residue: 0.9007 time to fit residues: 49.2463 Evaluate side-chains 56 residues out of total 237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 53 time to evaluate : 0.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain C residue 66 GLU Chi-restraints excluded: chain C residue 92 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 2 optimal weight: 10.0000 chunk 17 optimal weight: 6.9990 chunk 5 optimal weight: 10.0000 chunk 21 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 15 optimal weight: 10.0000 chunk 19 optimal weight: 0.9990 chunk 7 optimal weight: 0.9990 chunk 13 optimal weight: 5.9990 chunk 9 optimal weight: 7.9990 chunk 25 optimal weight: 0.8980 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 124 ASN C 124 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.122850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.103552 restraints weight = 2509.731| |-----------------------------------------------------------------------------| r_work (start): 0.3539 rms_B_bonded: 1.88 r_work: 0.3426 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3335 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8751 moved from start: 0.2086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 2202 Z= 0.151 Angle : 0.527 3.598 3000 Z= 0.296 Chirality : 0.049 0.119 360 Planarity : 0.004 0.036 369 Dihedral : 5.373 20.725 297 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 1.27 % Allowed : 18.57 % Favored : 80.17 % 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: -2.24 (0.48), residues: 264 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.70 (0.37), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 34 TYR 0.014 0.001 TYR B 114 PHE 0.009 0.001 PHE B 95 TRP 0.001 0.000 TRP C 79 HIS 0.002 0.001 HIS A 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.15 ( 2202) covalent geometry : angle 0.52656 / 0.30 ( 3000) hydrogen bonds : bond 0.02420 / 1.83 ( 39) hydrogen bonds : angle 5.16107 / 3.61 ( 117) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 51 time to evaluate : 0.085 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 52 average time/residue: 0.8750 time to fit residues: 46.1042 Evaluate side-chains 52 residues out of total 237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 50 time to evaluate : 0.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain C residue 66 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 25 optimal weight: 7.9990 chunk 19 optimal weight: 8.9990 chunk 10 optimal weight: 6.9990 chunk 6 optimal weight: 5.9990 chunk 23 optimal weight: 8.9990 chunk 3 optimal weight: 10.0000 chunk 7 optimal weight: 0.9990 chunk 14 optimal weight: 0.7980 chunk 4 optimal weight: 0.9980 chunk 1 optimal weight: 4.9990 chunk 24 optimal weight: 4.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 124 ASN C 124 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.123684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.103899 restraints weight = 2481.946| |-----------------------------------------------------------------------------| r_work (start): 0.3533 rms_B_bonded: 1.90 r_work: 0.3421 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3330 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8756 moved from start: 0.2139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 2202 Z= 0.158 Angle : 0.536 3.606 3000 Z= 0.301 Chirality : 0.049 0.119 360 Planarity : 0.005 0.042 369 Dihedral : 5.400 20.969 297 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 1.27 % Allowed : 17.72 % Favored : 81.01 % 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: -2.28 (0.48), residues: 264 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.73 (0.37), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 104 TYR 0.014 0.002 TYR B 114 PHE 0.009 0.002 PHE B 95 TRP 0.001 0.000 TRP C 79 HIS 0.002 0.001 HIS A 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.16 ( 2202) covalent geometry : angle 0.53640 / 0.30 ( 3000) hydrogen bonds : bond 0.02465 / 1.87 ( 39) hydrogen bonds : angle 5.15924 / 3.60 ( 117) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 48 time to evaluate : 0.087 Fit side-chains revert: symmetry clash REVERT: A 72 GLU cc_start: 0.8748 (mt-10) cc_final: 0.8411 (mt-10) outliers start: 3 outliers final: 2 residues processed: 50 average time/residue: 0.6872 time to fit residues: 34.8469 Evaluate side-chains 50 residues out of total 237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 48 time to evaluate : 0.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain C residue 66 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 17 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 9 optimal weight: 1.9990 chunk 20 optimal weight: 5.9990 chunk 22 optimal weight: 9.9990 chunk 3 optimal weight: 6.9990 chunk 10 optimal weight: 1.9990 chunk 18 optimal weight: 6.9990 chunk 11 optimal weight: 0.9990 chunk 2 optimal weight: 3.9990 chunk 25 optimal weight: 0.4980 overall best weight: 1.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 124 ASN C 124 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.124742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.105207 restraints weight = 2514.184| |-----------------------------------------------------------------------------| r_work (start): 0.3559 rms_B_bonded: 1.90 r_work: 0.3448 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3357 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8736 moved from start: 0.2130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 2202 Z= 0.131 Angle : 0.516 3.554 3000 Z= 0.288 Chirality : 0.049 0.119 360 Planarity : 0.005 0.044 369 Dihedral : 5.278 20.511 297 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 1.27 % Allowed : 17.72 % Favored : 81.01 % 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: -2.26 (0.48), residues: 264 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.72 (0.37), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 104 TYR 0.013 0.001 TYR B 114 PHE 0.008 0.001 PHE B 95 TRP 0.001 0.000 TRP C 79 HIS 0.002 0.000 HIS A 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 ( 2202) covalent geometry : angle 0.51565 / 0.29 ( 3000) hydrogen bonds : bond 0.02317 / 1.77 ( 39) hydrogen bonds : angle 5.02093 / 3.50 ( 117) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 49 time to evaluate : 0.090 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 51 average time/residue: 0.7138 time to fit residues: 36.8993 Evaluate side-chains 50 residues out of total 237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 48 time to evaluate : 0.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain C residue 66 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 6 optimal weight: 9.9990 chunk 24 optimal weight: 7.9990 chunk 2 optimal weight: 10.0000 chunk 25 optimal weight: 2.9990 chunk 1 optimal weight: 7.9990 chunk 17 optimal weight: 9.9990 chunk 10 optimal weight: 0.8980 chunk 18 optimal weight: 9.9990 chunk 0 optimal weight: 5.9990 chunk 26 optimal weight: 7.9990 chunk 22 optimal weight: 9.9990 overall best weight: 5.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 124 ASN C 124 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.118511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.099176 restraints weight = 2630.675| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 1.90 r_work: 0.3358 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3266 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8797 moved from start: 0.2198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 2202 Z= 0.271 Angle : 0.619 3.848 3000 Z= 0.351 Chirality : 0.051 0.122 360 Planarity : 0.006 0.054 369 Dihedral : 5.692 21.631 297 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.58 % Favored : 92.42 % Rotamer: Outliers : 0.84 % Allowed : 18.57 % Favored : 80.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.33 (0.48), residues: 264 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.77 (0.36), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.002 ARG B 104 TYR 0.017 0.002 TYR A 114 PHE 0.012 0.002 PHE B 95 TRP 0.003 0.001 TRP A 79 HIS 0.003 0.001 HIS B 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00637 / 0.27 ( 2202) covalent geometry : angle 0.61928 / 0.35 ( 3000) hydrogen bonds : bond 0.02909 / 2.15 ( 39) hydrogen bonds : angle 5.44907 / 3.78 ( 117) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1133.80 seconds wall clock time: 19 minutes 56.47 seconds (1196.47 seconds total)