Starting phenix.real_space_refine on Tue Feb 3 12:41:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9liw_63125/02_2026/9liw_63125.cif Found real_map, /net/cci-nas-00/data/ceres_data/9liw_63125/02_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_63125/02_2026/9liw_63125.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9liw_63125/02_2026/9liw_63125.map" model { file = "/net/cci-nas-00/data/ceres_data/9liw_63125/02_2026/9liw_63125.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9liw_63125/02_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-2.0-5952/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: 0.34, per 1000 atoms: 0.15 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: 0.10 Conformation dependent library (CDL) restraints added in 80.5 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: 0.05 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: 0.17 Time building geometry restraints manager: 0.15 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: 0.00 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: 4.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.060 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 2.920 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.980 ------------------------------------------------------------------------------- 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 covalent geometry : bond 0.00919 ( 2322) covalent geometry : angle 0.89789 ( 3168) SS BOND : bond 0.00743 ( 3) SS BOND : angle 0.73997 ( 6) hydrogen bonds : bond 0.21304 ( 12) hydrogen bonds : angle 8.64029 ( 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 : 0.086 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: 0.1126 time to fit residues: 4.2550 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 : 0.088 ------------------------------------------------------------------------------- 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 covalent geometry : bond 0.00389 ( 2322) covalent geometry : angle 0.62552 ( 3168) SS BOND : bond 0.00329 ( 3) SS BOND : angle 0.78376 ( 6) hydrogen bonds : bond 0.03263 ( 12) hydrogen bonds : angle 4.97606 ( 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 : 0.049 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: 0.0629 time to fit residues: 2.4875 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 : 0.050 ------------------------------------------------------------------------------- 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 covalent geometry : bond 0.00365 ( 2322) covalent geometry : angle 0.61310 ( 3168) SS BOND : bond 0.00306 ( 3) SS BOND : angle 0.70528 ( 6) hydrogen bonds : bond 0.02737 ( 12) hydrogen bonds : angle 4.25532 ( 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 : 0.086 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: 0.0953 time to fit residues: 4.1475 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 : 0.100 ------------------------------------------------------------------------------- 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 covalent geometry : bond 0.00447 ( 2322) covalent geometry : angle 0.63544 ( 3168) SS BOND : bond 0.00381 ( 3) SS BOND : angle 0.73848 ( 6) hydrogen bonds : bond 0.02502 ( 12) hydrogen bonds : angle 3.94296 ( 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 : 0.054 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: 0.0707 time to fit residues: 3.2263 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 : 0.051 ------------------------------------------------------------------------------- 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 covalent geometry : bond 0.00438 ( 2322) covalent geometry : angle 0.63302 ( 3168) SS BOND : bond 0.00367 ( 3) SS BOND : angle 0.77148 ( 6) hydrogen bonds : bond 0.02310 ( 12) hydrogen bonds : angle 3.79767 ( 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 : 0.051 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: 0.0678 time to fit residues: 2.9620 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 : 0.072 ------------------------------------------------------------------------------- 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 covalent geometry : bond 0.00195 ( 2322) covalent geometry : angle 0.57539 ( 3168) SS BOND : bond 0.00066 ( 3) SS BOND : angle 0.48162 ( 6) hydrogen bonds : bond 0.01707 ( 12) hydrogen bonds : angle 3.45768 ( 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 : 0.120 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: 0.1045 time to fit residues: 4.3891 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 : 0.050 ------------------------------------------------------------------------------- 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 covalent geometry : bond 0.00352 ( 2322) covalent geometry : angle 0.61395 ( 3168) SS BOND : bond 0.00288 ( 3) SS BOND : angle 0.61826 ( 6) hydrogen bonds : bond 0.01771 ( 12) hydrogen bonds : angle 3.39745 ( 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 : 0.053 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: 0.0674 time to fit residues: 2.6440 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 : 0.050 ------------------------------------------------------------------------------- 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 covalent geometry : bond 0.00283 ( 2322) covalent geometry : angle 0.59496 ( 3168) SS BOND : bond 0.00183 ( 3) SS BOND : angle 0.54816 ( 6) hydrogen bonds : bond 0.01700 ( 12) hydrogen bonds : angle 3.40091 ( 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 : 0.104 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: 0.1309 time to fit residues: 4.7763 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 : 0.141 ------------------------------------------------------------------------------- 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 covalent geometry : bond 0.00318 ( 2322) covalent geometry : angle 0.60699 ( 3168) SS BOND : bond 0.00221 ( 3) SS BOND : angle 0.61934 ( 6) hydrogen bonds : bond 0.01694 ( 12) hydrogen bonds : angle 3.38177 ( 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 : 0.053 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: 0.0726 time to fit residues: 2.5905 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 : 0.051 ------------------------------------------------------------------------------- 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 covalent geometry : bond 0.00402 ( 2322) covalent geometry : angle 0.63877 ( 3168) SS BOND : bond 0.00358 ( 3) SS BOND : angle 0.69159 ( 6) hydrogen bonds : bond 0.01832 ( 12) hydrogen bonds : angle 3.60898 ( 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 : 0.088 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: 0.0815 time to fit residues: 3.0316 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 : 0.103 ------------------------------------------------------------------------------- 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 covalent geometry : bond 0.00303 ( 2322) covalent geometry : angle 0.60854 ( 3168) SS BOND : bond 0.00202 ( 3) SS BOND : angle 0.58257 ( 6) hydrogen bonds : bond 0.01668 ( 12) hydrogen bonds : angle 3.46910 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 655.77 seconds wall clock time: 11 minutes 53.65 seconds (713.65 seconds total)