Starting phenix.real_space_refine on Wed Jun 3 09:43:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9liw_63125/06_2026/9liw_63125.cif Found real_map, /net/cci-nas-00/data/ceres_data/9liw_63125/06_2026/9liw_63125.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9liw_63125/06_2026/9liw_63125.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9liw_63125/06_2026/9liw_63125.map" model { file = "/net/cci-nas-00/data/ceres_data/9liw_63125/06_2026/9liw_63125.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9liw_63125/06_2026/9liw_63125.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 6 5.16 5 C 1401 2.51 5 N 390 2.21 5 O 471 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 2268 Number of models: 1 Model: "" Number of chains: 1 Chain: "AA" Number of atoms: 756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 756 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 6, 'TRANS': 95} Restraints were copied for chains: AB, AC Time building chain proxies: 0.50, per 1000 atoms: 0.22 Number of scatterers: 2268 At special positions: 0 Unit cell: (85.49, 83, 34.03, 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 6 16.00 O 471 8.00 N 390 7.00 C 1401 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYSAA 22 " - pdb=" SG CYSAA 89 " distance=2.02 Simple disulfide: pdb=" SG CYSAB 22 " - pdb=" SG CYSAB 89 " distance=2.02 Simple disulfide: pdb=" SG CYSAC 22 " - pdb=" SG CYSAC 89 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.18 Conformation dependent library (CDL) restraints added in 100.2 milliseconds 600 Ramachandran restraints generated. 300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 540 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 8 sheets defined 0.0% alpha, 11.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.09 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'AB' and resid 19 through 21 removed outlier: 6.344A pdb=" N THRAA 19 " --> pdb=" O ILEAC 20 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'AB' and resid 26 through 27 removed outlier: 6.248A pdb=" N TYRAA 26 " --> pdb=" O SERAC 27 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'AB' and resid 34 through 35 removed outlier: 6.616A pdb=" N VALAA 34 " --> pdb=" O ASNAB 35 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'AB' and resid 38 through 39 removed outlier: 6.427A pdb=" N ARGAA 38 " --> pdb=" O GLNAB 39 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'AB' and resid 64 through 65 removed outlier: 5.970A pdb=" N THRAA 64 " --> pdb=" O GLYAC 65 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'AB' and resid 74 through 76 removed outlier: 6.198A pdb=" N ALAAA 75 " --> pdb=" O ILEAC 76 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'AB' and resid 86 through 88 removed outlier: 6.170A pdb=" N ASPAA 86 " --> pdb=" O TYRAB 87 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'AB' and resid 106 through 108 removed outlier: 6.464A pdb=" N GLNAA 106 " --> pdb=" O LEUAC 107 " (cutoff:3.500A) 12 hydrogen bonds defined for protein. 36 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: 0.27 Time building geometry restraints manager: 0.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 756 1.34 - 1.45: 383 1.45 - 1.57: 1177 1.57 - 1.68: 0 1.68 - 1.80: 6 Bond restraints: 2322 Sorted by residual: bond pdb=" CG1 ILEAA 29 " pdb=" CD1 ILEAA 29 " ideal model delta sigma weight residual 1.513 1.428 0.085 3.90e-02 6.57e+02 4.73e+00 bond pdb=" CG1 ILEAB 29 " pdb=" CD1 ILEAB 29 " ideal model delta sigma weight residual 1.513 1.428 0.085 3.90e-02 6.57e+02 4.71e+00 bond pdb=" CG1 ILEAC 29 " pdb=" CD1 ILEAC 29 " ideal model delta sigma weight residual 1.513 1.428 0.085 3.90e-02 6.57e+02 4.71e+00 bond pdb=" CB ARGAA 58 " pdb=" CG ARGAA 58 " ideal model delta sigma weight residual 1.520 1.470 0.050 3.00e-02 1.11e+03 2.83e+00 bond pdb=" CB ARGAC 58 " pdb=" CG ARGAC 58 " ideal model delta sigma weight residual 1.520 1.470 0.050 3.00e-02 1.11e+03 2.77e+00 ... (remaining 2317 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.58: 2952 1.58 - 3.16: 177 3.16 - 4.73: 36 4.73 - 6.31: 0 6.31 - 7.89: 3 Bond angle restraints: 3168 Sorted by residual: angle pdb=" C GLYAC 12 " pdb=" N THRAC 13 " pdb=" CA THRAC 13 " ideal model delta sigma weight residual 122.37 119.40 2.97 9.30e-01 1.16e+00 1.02e+01 angle pdb=" C GLYAA 12 " pdb=" N THRAA 13 " pdb=" CA THRAA 13 " ideal model delta sigma weight residual 122.37 119.41 2.96 9.30e-01 1.16e+00 1.01e+01 angle pdb=" C GLYAB 12 " pdb=" N THRAB 13 " pdb=" CA THRAB 13 " ideal model delta sigma weight residual 122.37 119.43 2.94 9.30e-01 1.16e+00 1.00e+01 angle pdb=" CA PROAC 99 " pdb=" C PROAC 99 " pdb=" N VALAC 100 " ideal model delta sigma weight residual 114.74 117.84 -3.10 1.03e+00 9.43e-01 9.06e+00 angle pdb=" CA PROAA 99 " pdb=" C PROAA 99 " pdb=" N VALAA 100 " ideal model delta sigma weight residual 114.74 117.83 -3.09 1.03e+00 9.43e-01 9.02e+00 ... (remaining 3163 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 10.92: 1125 10.92 - 21.84: 156 21.84 - 32.76: 63 32.76 - 43.68: 15 43.68 - 54.59: 9 Dihedral angle restraints: 1368 sinusoidal: 507 harmonic: 861 Sorted by residual: dihedral pdb=" CA SERAA 57 " pdb=" C SERAA 57 " pdb=" N ARGAA 58 " pdb=" CA ARGAA 58 " ideal model delta harmonic sigma weight residual 180.00 154.06 25.94 0 5.00e+00 4.00e-02 2.69e+01 dihedral pdb=" CA SERAC 57 " pdb=" C SERAC 57 " pdb=" N ARGAC 58 " pdb=" CA ARGAC 58 " ideal model delta harmonic sigma weight residual 180.00 154.09 25.91 0 5.00e+00 4.00e-02 2.68e+01 dihedral pdb=" CA SERAB 57 " pdb=" C SERAB 57 " pdb=" N ARGAB 58 " pdb=" CA ARGAB 58 " ideal model delta harmonic sigma weight residual 180.00 154.10 25.90 0 5.00e+00 4.00e-02 2.68e+01 ... (remaining 1365 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 207 0.037 - 0.073: 78 0.073 - 0.110: 41 0.110 - 0.147: 13 0.147 - 0.183: 6 Chirality restraints: 345 Sorted by residual: chirality pdb=" CB THRAB 13 " pdb=" CA THRAB 13 " pdb=" OG1 THRAB 13 " pdb=" CG2 THRAB 13 " both_signs ideal model delta sigma weight residual False 2.55 2.37 0.18 2.00e-01 2.50e+01 8.42e-01 chirality pdb=" CB THRAA 13 " pdb=" CA THRAA 13 " pdb=" OG1 THRAA 13 " pdb=" CG2 THRAA 13 " both_signs ideal model delta sigma weight residual False 2.55 2.38 0.18 2.00e-01 2.50e+01 7.75e-01 chirality pdb=" CB THRAC 13 " pdb=" CA THRAC 13 " pdb=" OG1 THRAC 13 " pdb=" CG2 THRAC 13 " both_signs ideal model delta sigma weight residual False 2.55 2.38 0.18 2.00e-01 2.50e+01 7.66e-01 ... (remaining 342 not shown) Planarity restraints: 417 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLYAA 98 " 0.052 5.00e-02 4.00e+02 7.90e-02 9.99e+00 pdb=" N PROAA 99 " -0.137 5.00e-02 4.00e+02 pdb=" CA PROAA 99 " 0.042 5.00e-02 4.00e+02 pdb=" CD PROAA 99 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLYAC 98 " 0.052 5.00e-02 4.00e+02 7.89e-02 9.97e+00 pdb=" N PROAC 99 " -0.137 5.00e-02 4.00e+02 pdb=" CA PROAC 99 " 0.042 5.00e-02 4.00e+02 pdb=" CD PROAC 99 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLYAB 98 " 0.052 5.00e-02 4.00e+02 7.88e-02 9.94e+00 pdb=" N PROAB 99 " -0.136 5.00e-02 4.00e+02 pdb=" CA PROAB 99 " 0.042 5.00e-02 4.00e+02 pdb=" CD PROAB 99 " 0.043 5.00e-02 4.00e+02 ... (remaining 414 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.85: 855 2.85 - 3.36: 1916 3.36 - 3.87: 3664 3.87 - 4.39: 4105 4.39 - 4.90: 8155 Nonbonded interactions: 18695 Sorted by model distance: nonbonded pdb=" O GLUAA 82 " pdb=" N GLUAC 82 " model vdw 2.334 3.120 nonbonded pdb=" N GLUAA 82 " pdb=" O GLUAB 82 " model vdw 2.335 3.120 nonbonded pdb=" O GLYAA 15 " pdb=" NH1 ARGAA 17 " model vdw 2.355 3.120 nonbonded pdb=" O GLYAC 15 " pdb=" NH1 ARGAC 17 " model vdw 2.355 3.120 nonbonded pdb=" O GLYAB 15 " pdb=" NH1 ARGAB 17 " model vdw 2.355 3.120 ... (remaining 18690 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'AA' selection = chain 'AB' selection = chain 'AC' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.950 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: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 3.930 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:1.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 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 : 0.009 0.085 2325 Z= 0.419 Angle : 0.898 7.891 3174 Z= 0.521 Chirality : 0.053 0.183 345 Planarity : 0.008 0.079 417 Dihedral : 12.480 54.594 819 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Rotamer: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % 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: -6.04 (0.27), residues: 300 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.59 (0.21), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.002 ARGAC 58 TYR 0.017 0.002 TYRAC 87 PHE 0.008 0.002 PHEAC 63 TRP 0.013 0.002 TRPAB 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00919 / 0.42 ( 2322) covalent geometry : angle 0.89789 / 0.52 ( 3168) SS BOND : bond 0.00743 / 0.47 ( 3) SS BOND : angle 0.73997 / 0.44 ( 6) hydrogen bonds : bond 0.21304 / 14.93 ( 12) hydrogen bonds : angle 8.64029 / 5.27 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 600 Ramachandran restraints generated. 300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 600 Ramachandran restraints generated. 300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 34 time to evaluate : 0.094 Fit side-chains REVERT: AB 55 ARG cc_start: 0.7980 (mtm-85) cc_final: 0.7323 (mmp-170) REVERT: AB 62 ARG cc_start: 0.7756 (ttp80) cc_final: 0.6788 (mmp-170) outliers start: 0 outliers final: 0 residues processed: 34 average time/residue: 0.1110 time to fit residues: 4.2479 Evaluate side-chains 23 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 23 time to evaluate : 0.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 27 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 13 optimal weight: 5.9990 chunk 1 optimal weight: 0.0370 chunk 8 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 overall best weight: 1.8066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.102825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.089042 restraints weight = 3666.458| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 2.35 r_work: 0.3397 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3280 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8749 moved from start: 0.1206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 2325 Z= 0.163 Angle : 0.626 9.531 3174 Z= 0.299 Chirality : 0.045 0.213 345 Planarity : 0.007 0.075 417 Dihedral : 4.273 19.803 336 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 0.00 % Allowed : 10.04 % Favored : 89.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.54 (0.29), residues: 300 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.22 (0.22), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARGAB 58 TYR 0.013 0.002 TYRAC 88 PHE 0.006 0.001 PHEAC 101 TRP 0.010 0.001 TRPAB 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.16 ( 2322) covalent geometry : angle 0.62552 / 0.30 ( 3168) SS BOND : bond 0.00329 / 0.21 ( 3) SS BOND : angle 0.78376 / 0.46 ( 6) hydrogen bonds : bond 0.03263 / 2.20 ( 12) hydrogen bonds : angle 4.97606 / 2.98 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 600 Ramachandran restraints generated. 300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 600 Ramachandran restraints generated. 300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 0.087 Fit side-chains REVERT: AA 58 ARG cc_start: 0.7314 (mtt180) cc_final: 0.6967 (mtm110) REVERT: AA 94 ASP cc_start: 0.8787 (t0) cc_final: 0.8447 (t0) REVERT: AB 55 ARG cc_start: 0.8422 (mtm-85) cc_final: 0.7265 (mmp-170) REVERT: AB 62 ARG cc_start: 0.8068 (ttp80) cc_final: 0.6386 (mmp80) REVERT: AB 94 ASP cc_start: 0.8607 (t70) cc_final: 0.8337 (t70) outliers start: 0 outliers final: 0 residues processed: 35 average time/residue: 0.0987 time to fit residues: 3.8941 Evaluate side-chains 32 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 16 optimal weight: 5.9990 chunk 14 optimal weight: 0.6980 chunk 29 optimal weight: 6.9990 chunk 18 optimal weight: 3.9990 chunk 26 optimal weight: 7.9990 chunk 19 optimal weight: 5.9990 chunk 7 optimal weight: 9.9990 chunk 21 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 9 optimal weight: 0.7980 chunk 15 optimal weight: 3.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.102736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.089563 restraints weight = 3681.822| |-----------------------------------------------------------------------------| r_work (start): 0.3537 rms_B_bonded: 2.26 r_work: 0.3426 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3315 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8729 moved from start: 0.1545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 2325 Z= 0.154 Angle : 0.613 10.158 3174 Z= 0.289 Chirality : 0.045 0.231 345 Planarity : 0.007 0.066 417 Dihedral : 3.911 19.661 336 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 1.20 % Allowed : 12.05 % Favored : 86.75 % 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: -5.34 (0.31), residues: 300 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.07 (0.23), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARGAB 58 TYR 0.015 0.002 TYRAB 37 PHE 0.006 0.001 PHEAC 101 TRP 0.012 0.001 TRPAB 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.15 ( 2322) covalent geometry : angle 0.61310 / 0.29 ( 3168) SS BOND : bond 0.00306 / 0.19 ( 3) SS BOND : angle 0.70528 / 0.42 ( 6) hydrogen bonds : bond 0.02737 / 1.85 ( 12) hydrogen bonds : angle 4.25532 / 2.55 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 600 Ramachandran restraints generated. 300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 600 Ramachandran restraints generated. 300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 38 time to evaluate : 0.111 Fit side-chains REVERT: AA 94 ASP cc_start: 0.8806 (t0) cc_final: 0.8360 (t0) REVERT: AB 55 ARG cc_start: 0.8425 (mtm-85) cc_final: 0.7196 (mmp-170) REVERT: AB 58 ARG cc_start: 0.4922 (mmm160) cc_final: 0.4647 (mmm160) REVERT: AB 62 ARG cc_start: 0.8055 (ttp80) cc_final: 0.6469 (mmp-170) REVERT: AB 94 ASP cc_start: 0.8630 (t70) cc_final: 0.8287 (t70) outliers start: 3 outliers final: 3 residues processed: 39 average time/residue: 0.1214 time to fit residues: 5.2458 Evaluate side-chains 39 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 36 time to evaluate : 0.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AA residue 95 SER Chi-restraints excluded: chain AB residue 95 SER Chi-restraints excluded: chain AC residue 43 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 9 optimal weight: 5.9990 chunk 11 optimal weight: 7.9990 chunk 29 optimal weight: 3.9990 chunk 4 optimal weight: 8.9990 chunk 28 optimal weight: 4.9990 chunk 14 optimal weight: 0.9990 chunk 1 optimal weight: 0.9990 chunk 10 optimal weight: 9.9990 chunk 3 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.100931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.087985 restraints weight = 3663.284| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 2.27 r_work: 0.3404 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3285 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8745 moved from start: 0.1804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 2325 Z= 0.187 Angle : 0.636 10.183 3174 Z= 0.301 Chirality : 0.046 0.260 345 Planarity : 0.007 0.067 417 Dihedral : 3.818 19.500 336 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 1.61 % Allowed : 16.87 % Favored : 81.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.26 (0.31), residues: 300 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.01 (0.24), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARGAB 58 TYR 0.015 0.002 TYRAB 37 PHE 0.004 0.001 PHEAA 63 TRP 0.012 0.001 TRPAB 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00447 / 0.19 ( 2322) covalent geometry : angle 0.63544 / 0.30 ( 3168) SS BOND : bond 0.00381 / 0.24 ( 3) SS BOND : angle 0.73848 / 0.43 ( 6) hydrogen bonds : bond 0.02502 / 1.68 ( 12) hydrogen bonds : angle 3.94296 / 2.36 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 600 Ramachandran restraints generated. 300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 600 Ramachandran restraints generated. 300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 40 time to evaluate : 0.065 Fit side-chains REVERT: AA 58 ARG cc_start: 0.7777 (mtm110) cc_final: 0.7473 (mtp-110) REVERT: AA 94 ASP cc_start: 0.8822 (t0) cc_final: 0.8415 (t0) REVERT: AB 55 ARG cc_start: 0.8438 (mtm-85) cc_final: 0.7213 (mmp-170) REVERT: AB 58 ARG cc_start: 0.4846 (mmm160) cc_final: 0.4571 (mmm160) REVERT: AB 62 ARG cc_start: 0.8093 (ttp80) cc_final: 0.6448 (mmp-170) REVERT: AB 94 ASP cc_start: 0.8634 (t70) cc_final: 0.8265 (t70) outliers start: 4 outliers final: 4 residues processed: 41 average time/residue: 0.1150 time to fit residues: 5.2102 Evaluate side-chains 42 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 38 time to evaluate : 0.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AA residue 43 THR Chi-restraints excluded: chain AA residue 95 SER Chi-restraints excluded: chain AB residue 95 SER Chi-restraints excluded: chain AC residue 43 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 4 optimal weight: 8.9990 chunk 24 optimal weight: 4.9990 chunk 22 optimal weight: 7.9990 chunk 15 optimal weight: 4.9990 chunk 28 optimal weight: 7.9990 chunk 11 optimal weight: 6.9990 chunk 2 optimal weight: 2.9990 chunk 8 optimal weight: 0.7980 chunk 20 optimal weight: 0.9980 chunk 18 optimal weight: 0.9990 chunk 6 optimal weight: 5.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.101274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.089052 restraints weight = 3662.727| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 2.17 r_work: 0.3436 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3320 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8758 moved from start: 0.1968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 2325 Z= 0.184 Angle : 0.633 10.453 3174 Z= 0.299 Chirality : 0.046 0.276 345 Planarity : 0.007 0.067 417 Dihedral : 3.745 19.682 336 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 2.81 % Allowed : 16.06 % Favored : 81.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.23 (0.31), residues: 300 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.98 (0.24), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARGAB 58 TYR 0.015 0.002 TYRAB 37 PHE 0.005 0.001 PHEAC 101 TRP 0.012 0.001 TRPAB 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00438 / 0.18 ( 2322) covalent geometry : angle 0.63302 / 0.30 ( 3168) SS BOND : bond 0.00367 / 0.23 ( 3) SS BOND : angle 0.77148 / 0.45 ( 6) hydrogen bonds : bond 0.02310 / 1.53 ( 12) hydrogen bonds : angle 3.79767 / 2.28 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 600 Ramachandran restraints generated. 300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 600 Ramachandran restraints generated. 300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 34 time to evaluate : 0.053 Fit side-chains revert: symmetry clash REVERT: AA 29 ILE cc_start: 0.8165 (OUTLIER) cc_final: 0.7840 (pt) REVERT: AA 94 ASP cc_start: 0.8785 (t0) cc_final: 0.8409 (t0) REVERT: AB 55 ARG cc_start: 0.8427 (mtm-85) cc_final: 0.7242 (mmp-170) REVERT: AB 58 ARG cc_start: 0.4840 (mmm160) cc_final: 0.4528 (mmm160) REVERT: AB 62 ARG cc_start: 0.8086 (ttp80) cc_final: 0.6506 (mmp-170) REVERT: AB 94 ASP cc_start: 0.8560 (t70) cc_final: 0.8193 (t70) outliers start: 7 outliers final: 4 residues processed: 39 average time/residue: 0.0953 time to fit residues: 4.1115 Evaluate side-chains 38 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 33 time to evaluate : 0.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AA residue 29 ILE Chi-restraints excluded: chain AA residue 43 THR Chi-restraints excluded: chain AA residue 95 SER Chi-restraints excluded: chain AB residue 95 SER Chi-restraints excluded: chain AC residue 43 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 13 optimal weight: 0.0570 chunk 4 optimal weight: 8.9990 chunk 9 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 chunk 26 optimal weight: 6.9990 chunk 25 optimal weight: 0.0050 chunk 27 optimal weight: 5.9990 chunk 14 optimal weight: 1.9990 chunk 23 optimal weight: 0.0670 chunk 8 optimal weight: 0.7980 overall best weight: 0.3852 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.114870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.102597 restraints weight = 3553.465| |-----------------------------------------------------------------------------| r_work (start): 0.3668 rms_B_bonded: 2.31 r_work: 0.3558 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3438 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 moved from start: 0.2574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 2325 Z= 0.084 Angle : 0.575 10.060 3174 Z= 0.263 Chirality : 0.044 0.289 345 Planarity : 0.006 0.065 417 Dihedral : 3.318 16.907 336 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 0.40 % Allowed : 18.88 % Favored : 80.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.02 (0.33), residues: 300 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.82 (0.25), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARGAC 38 TYR 0.016 0.002 TYRAB 37 PHE 0.010 0.001 PHEAC 101 TRP 0.003 0.001 TRPAB 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00195 / 0.08 ( 2322) covalent geometry : angle 0.57539 / 0.26 ( 3168) SS BOND : bond 0.00066 / 0.04 ( 3) SS BOND : angle 0.48162 / 0.31 ( 6) hydrogen bonds : bond 0.01707 / 1.18 ( 12) hydrogen bonds : angle 3.45768 / 2.10 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 600 Ramachandran restraints generated. 300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 600 Ramachandran restraints generated. 300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 38 time to evaluate : 0.066 Fit side-chains REVERT: AA 55 ARG cc_start: 0.8416 (mtm180) cc_final: 0.8110 (mtm-85) REVERT: AA 94 ASP cc_start: 0.8748 (t0) cc_final: 0.8337 (t0) REVERT: AB 55 ARG cc_start: 0.8388 (mtm-85) cc_final: 0.7062 (mmp-170) REVERT: AB 58 ARG cc_start: 0.4450 (mmm160) cc_final: 0.4213 (mmm160) REVERT: AB 62 ARG cc_start: 0.8014 (ttp80) cc_final: 0.6393 (mmp-170) REVERT: AB 82 GLU cc_start: 0.8471 (mm-30) cc_final: 0.6644 (pm20) REVERT: AB 94 ASP cc_start: 0.8454 (t70) cc_final: 0.8043 (t0) REVERT: AC 29 ILE cc_start: 0.7620 (pt) cc_final: 0.7304 (pt) outliers start: 1 outliers final: 1 residues processed: 38 average time/residue: 0.0975 time to fit residues: 4.1333 Evaluate side-chains 37 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 36 time to evaluate : 0.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AA residue 95 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 21 optimal weight: 8.9990 chunk 10 optimal weight: 6.9990 chunk 13 optimal weight: 7.9990 chunk 28 optimal weight: 0.0770 chunk 4 optimal weight: 8.9990 chunk 20 optimal weight: 5.9990 chunk 19 optimal weight: 3.9990 chunk 22 optimal weight: 7.9990 chunk 16 optimal weight: 0.0470 chunk 3 optimal weight: 2.9990 chunk 26 optimal weight: 0.8980 overall best weight: 1.6040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.105540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.093061 restraints weight = 3697.807| |-----------------------------------------------------------------------------| r_work (start): 0.3609 rms_B_bonded: 2.28 r_work: 0.3508 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3396 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8707 moved from start: 0.2448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 2325 Z= 0.147 Angle : 0.614 10.393 3174 Z= 0.287 Chirality : 0.046 0.329 345 Planarity : 0.006 0.058 417 Dihedral : 3.366 17.973 336 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 0.80 % Allowed : 19.28 % Favored : 79.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.01 (0.33), residues: 300 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.81 (0.25), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARGAC 55 TYR 0.017 0.002 TYRAB 37 PHE 0.003 0.001 PHEAA 63 TRP 0.013 0.001 TRPAB 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.15 ( 2322) covalent geometry : angle 0.61395 / 0.29 ( 3168) SS BOND : bond 0.00288 / 0.18 ( 3) SS BOND : angle 0.61826 / 0.35 ( 6) hydrogen bonds : bond 0.01771 / 1.15 ( 12) hydrogen bonds : angle 3.39745 / 2.06 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 600 Ramachandran restraints generated. 300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 600 Ramachandran restraints generated. 300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 35 time to evaluate : 0.063 Fit side-chains REVERT: AA 94 ASP cc_start: 0.8756 (t0) cc_final: 0.8361 (t0) REVERT: AB 55 ARG cc_start: 0.8433 (mtm-85) cc_final: 0.7116 (mmp-170) REVERT: AB 58 ARG cc_start: 0.4529 (mmm160) cc_final: 0.4203 (mmm160) REVERT: AB 62 ARG cc_start: 0.8030 (ttp80) cc_final: 0.6494 (mmp-170) REVERT: AB 82 GLU cc_start: 0.8500 (mm-30) cc_final: 0.6854 (mp0) REVERT: AB 94 ASP cc_start: 0.8538 (t70) cc_final: 0.8113 (t0) REVERT: AC 29 ILE cc_start: 0.7853 (pt) cc_final: 0.7469 (pt) outliers start: 2 outliers final: 2 residues processed: 35 average time/residue: 0.1190 time to fit residues: 4.6309 Evaluate side-chains 36 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 34 time to evaluate : 0.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AA residue 95 SER Chi-restraints excluded: chain AB residue 95 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 8 optimal weight: 1.9990 chunk 6 optimal weight: 7.9990 chunk 5 optimal weight: 0.9990 chunk 17 optimal weight: 7.9990 chunk 25 optimal weight: 0.8980 chunk 15 optimal weight: 0.9990 chunk 2 optimal weight: 7.9990 chunk 14 optimal weight: 2.9990 chunk 18 optimal weight: 0.9980 chunk 21 optimal weight: 7.9990 chunk 9 optimal weight: 5.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.110132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.097979 restraints weight = 3542.606| |-----------------------------------------------------------------------------| r_work (start): 0.3641 rms_B_bonded: 2.30 r_work: 0.3556 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3447 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8711 moved from start: 0.2523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 2325 Z= 0.116 Angle : 0.595 10.655 3174 Z= 0.273 Chirality : 0.045 0.285 345 Planarity : 0.006 0.065 417 Dihedral : 3.288 17.914 336 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 0.80 % Allowed : 19.68 % Favored : 79.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.95 (0.33), residues: 300 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.77 (0.25), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARGAA 58 TYR 0.017 0.002 TYRAB 37 PHE 0.006 0.001 PHEAC 101 TRP 0.009 0.001 TRPAB 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.12 ( 2322) covalent geometry : angle 0.59496 / 0.27 ( 3168) SS BOND : bond 0.00183 / 0.12 ( 3) SS BOND : angle 0.54816 / 0.32 ( 6) hydrogen bonds : bond 0.01700 / 1.13 ( 12) hydrogen bonds : angle 3.40091 / 2.06 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 600 Ramachandran restraints generated. 300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 600 Ramachandran restraints generated. 300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 33 time to evaluate : 0.090 Fit side-chains REVERT: AA 94 ASP cc_start: 0.8717 (t0) cc_final: 0.8337 (t0) REVERT: AB 55 ARG cc_start: 0.8406 (mtm-85) cc_final: 0.7162 (mmp-170) REVERT: AB 58 ARG cc_start: 0.4578 (mmm160) cc_final: 0.4207 (mmm160) REVERT: AB 62 ARG cc_start: 0.8068 (ttp80) cc_final: 0.6523 (mmp-170) REVERT: AB 82 GLU cc_start: 0.8516 (mm-30) cc_final: 0.6914 (mp0) REVERT: AB 94 ASP cc_start: 0.8494 (t70) cc_final: 0.8072 (t0) REVERT: AC 29 ILE cc_start: 0.7822 (pt) cc_final: 0.7434 (pt) outliers start: 2 outliers final: 2 residues processed: 33 average time/residue: 0.1155 time to fit residues: 4.2063 Evaluate side-chains 35 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 33 time to evaluate : 0.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AA residue 95 SER Chi-restraints excluded: chain AB residue 95 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 14 optimal weight: 4.9990 chunk 16 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 5 optimal weight: 8.9990 chunk 1 optimal weight: 4.9990 chunk 28 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 7 optimal weight: 7.9990 chunk 10 optimal weight: 0.0070 chunk 6 optimal weight: 1.9990 overall best weight: 1.4004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.109305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.097082 restraints weight = 3599.339| |-----------------------------------------------------------------------------| r_work (start): 0.3621 rms_B_bonded: 2.28 r_work: 0.3519 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3406 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8686 moved from start: 0.2466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2325 Z= 0.132 Angle : 0.607 10.880 3174 Z= 0.282 Chirality : 0.047 0.314 345 Planarity : 0.006 0.058 417 Dihedral : 3.334 17.609 336 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 0.80 % Allowed : 20.88 % Favored : 78.31 % 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: -4.92 (0.33), residues: 300 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.75 (0.25), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARGAC 62 TYR 0.018 0.002 TYRAB 37 PHE 0.004 0.001 PHEAC 101 TRP 0.011 0.001 TRPAB 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.13 ( 2322) covalent geometry : angle 0.60699 / 0.28 ( 3168) SS BOND : bond 0.00221 / 0.14 ( 3) SS BOND : angle 0.61934 / 0.36 ( 6) hydrogen bonds : bond 0.01694 / 1.10 ( 12) hydrogen bonds : angle 3.38177 / 2.04 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 600 Ramachandran restraints generated. 300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 600 Ramachandran restraints generated. 300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 32 time to evaluate : 0.086 Fit side-chains REVERT: AA 94 ASP cc_start: 0.8731 (t0) cc_final: 0.8333 (t0) REVERT: AB 55 ARG cc_start: 0.8392 (mtm-85) cc_final: 0.7068 (mmp-170) REVERT: AB 58 ARG cc_start: 0.4739 (mmm160) cc_final: 0.4233 (mmm160) REVERT: AB 62 ARG cc_start: 0.8035 (ttp80) cc_final: 0.6438 (mmp-170) REVERT: AB 82 GLU cc_start: 0.8475 (mm-30) cc_final: 0.6849 (mp0) REVERT: AB 94 ASP cc_start: 0.8450 (t70) cc_final: 0.7996 (t0) REVERT: AC 29 ILE cc_start: 0.7825 (pt) cc_final: 0.7462 (pt) outliers start: 2 outliers final: 2 residues processed: 32 average time/residue: 0.1254 time to fit residues: 4.4276 Evaluate side-chains 34 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 32 time to evaluate : 0.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AA residue 95 SER Chi-restraints excluded: chain AB residue 95 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 17 optimal weight: 6.9990 chunk 15 optimal weight: 7.9990 chunk 14 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 6 optimal weight: 5.9990 chunk 29 optimal weight: 0.6980 chunk 19 optimal weight: 4.9990 chunk 2 optimal weight: 7.9990 chunk 3 optimal weight: 2.9990 chunk 21 optimal weight: 8.9990 chunk 8 optimal weight: 0.7980 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.107562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.095143 restraints weight = 3678.298| |-----------------------------------------------------------------------------| r_work (start): 0.3586 rms_B_bonded: 2.26 r_work: 0.3486 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3376 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8711 moved from start: 0.2502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 2325 Z= 0.167 Angle : 0.639 11.034 3174 Z= 0.299 Chirality : 0.046 0.297 345 Planarity : 0.006 0.064 417 Dihedral : 3.517 19.018 336 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 1.20 % Allowed : 20.48 % Favored : 78.31 % 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: -4.94 (0.33), residues: 300 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.76 (0.25), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARGAC 62 TYR 0.017 0.002 TYRAB 37 PHE 0.004 0.001 PHEAC 63 TRP 0.013 0.001 TRPAB 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00402 / 0.17 ( 2322) covalent geometry : angle 0.63877 / 0.30 ( 3168) SS BOND : bond 0.00358 / 0.22 ( 3) SS BOND : angle 0.69159 / 0.40 ( 6) hydrogen bonds : bond 0.01832 / 1.16 ( 12) hydrogen bonds : angle 3.60898 / 2.17 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 600 Ramachandran restraints generated. 300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 600 Ramachandran restraints generated. 300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 32 time to evaluate : 0.090 Fit side-chains REVERT: AB 55 ARG cc_start: 0.8368 (mtm-85) cc_final: 0.7164 (mmp-170) REVERT: AB 58 ARG cc_start: 0.4974 (mmm160) cc_final: 0.4385 (mmm160) REVERT: AB 62 ARG cc_start: 0.7976 (ttp80) cc_final: 0.6455 (mmp-170) REVERT: AB 82 GLU cc_start: 0.8468 (mm-30) cc_final: 0.6872 (mp0) REVERT: AB 94 ASP cc_start: 0.8491 (t70) cc_final: 0.7968 (t0) outliers start: 3 outliers final: 3 residues processed: 33 average time/residue: 0.1010 time to fit residues: 3.7770 Evaluate side-chains 35 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 32 time to evaluate : 0.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AA residue 95 SER Chi-restraints excluded: chain AB residue 29 ILE Chi-restraints excluded: chain AB residue 95 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 18 optimal weight: 1.9990 chunk 28 optimal weight: 4.9990 chunk 14 optimal weight: 4.9990 chunk 7 optimal weight: 2.9990 chunk 22 optimal weight: 6.9990 chunk 21 optimal weight: 7.9990 chunk 19 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 chunk 29 optimal weight: 0.4980 chunk 11 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.109323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.096949 restraints weight = 3621.678| |-----------------------------------------------------------------------------| r_work (start): 0.3623 rms_B_bonded: 2.26 r_work: 0.3541 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3434 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8717 moved from start: 0.2650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2325 Z= 0.125 Angle : 0.608 11.044 3174 Z= 0.280 Chirality : 0.046 0.293 345 Planarity : 0.006 0.061 417 Dihedral : 3.371 18.107 336 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 0.80 % Allowed : 21.29 % Favored : 77.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.90 (0.33), residues: 300 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.73 (0.25), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARGAC 38 TYR 0.018 0.002 TYRAB 37 PHE 0.005 0.001 PHEAC 101 TRP 0.009 0.001 TRPAB 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.13 ( 2322) covalent geometry : angle 0.60854 / 0.28 ( 3168) SS BOND : bond 0.00202 / 0.13 ( 3) SS BOND : angle 0.58257 / 0.34 ( 6) hydrogen bonds : bond 0.01668 / 1.09 ( 12) hydrogen bonds : angle 3.46910 / 2.09 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 843.59 seconds wall clock time: 15 minutes 9.84 seconds (909.84 seconds total)