Starting phenix.real_space_refine on Wed Jun 3 09:43:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9liv_63124/06_2026/9liv_63124.cif Found real_map, /net/cci-nas-00/data/ceres_data/9liv_63124/06_2026/9liv_63124.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9liv_63124/06_2026/9liv_63124.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9liv_63124/06_2026/9liv_63124.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9liv_63124/06_2026/9liv_63124.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9liv_63124/06_2026/9liv_63124.map" } resolution = 3.1 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 27 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: 0.69, per 1000 atoms: 0.30 Number of scatterers: 2268 At special positions: 0 Unit cell: (97.11, 77.19, 36.52, 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=2.03 Simple disulfide: pdb=" SG CYSAB 22 " - pdb=" SG CYSAB 89 " distance=2.03 Simple disulfide: pdb=" SG CYSAC 22 " - pdb=" SG CYSAC 89 " distance=2.03 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 106.8 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 9 sheets defined 0.0% alpha, 23.5% 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 17 through 22 removed outlier: 6.287A pdb=" N ARGAA 17 " --> pdb=" O VALAB 18 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N ILEAB 20 " --> pdb=" O ARGAA 17 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N THRAA 19 " --> pdb=" O ILEAB 20 " (cutoff:3.500A) removed outlier: 7.969A pdb=" N CYSAB 22 " --> pdb=" O THRAA 19 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N SERAA 21 " --> pdb=" O CYSAB 22 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'AB' and resid 27 through 29 removed outlier: 6.778A pdb=" N ASNAA 28 " --> pdb=" O ILEAB 29 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N ASNAC 28 " --> pdb=" O SERAA 27 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'AB' and resid 32 through 34 Processing sheet with id=AA4, first strand: chain 'AB' and resid 37 through 38 removed outlier: 6.350A pdb=" N TYRAA 37 " --> pdb=" O ARGAB 38 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'AB' and resid 46 through 49 removed outlier: 9.089A pdb=" N LYSAA 46 " --> pdb=" O VALAB 47 " (cutoff:3.500A) removed outlier: 9.833A pdb=" N ILEAB 49 " --> pdb=" O LYSAA 46 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N LEUAA 48 " --> pdb=" O ILEAB 49 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N VALAA 47 " --> pdb=" O LYSAC 46 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N LEUAC 48 " --> pdb=" O VALAA 47 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'AB' and resid 53 through 54 removed outlier: 6.650A pdb=" N ASNAA 53 " --> pdb=" O TYRAB 54 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'AB' and resid 74 through 80 removed outlier: 6.305A pdb=" N ALAAA 75 " --> pdb=" O ILEAB 76 " (cutoff:3.500A) removed outlier: 8.187A pdb=" N GLYAB 78 " --> pdb=" O ALAAA 75 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N SERAA 77 " --> pdb=" O GLYAB 78 " (cutoff:3.500A) removed outlier: 8.481A pdb=" N GLNAB 80 " --> pdb=" O SERAA 77 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N LEUAA 79 " --> pdb=" O GLNAB 80 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'AB' and resid 86 through 88 removed outlier: 6.485A pdb=" N ASPAA 86 " --> pdb=" O TYRAC 87 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'AB' and resid 106 through 108 removed outlier: 6.443A pdb=" N GLNAA 106 " --> pdb=" O LEUAB 107 " (cutoff:3.500A) 23 hydrogen bonds defined for protein. 69 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: 0.32 Time building geometry restraints manager: 0.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 756 1.34 - 1.45: 406 1.45 - 1.57: 1154 1.57 - 1.68: 0 1.68 - 1.80: 6 Bond restraints: 2322 Sorted by residual: bond pdb=" C LEUAB 40 " pdb=" N PROAB 41 " ideal model delta sigma weight residual 1.334 1.317 0.017 8.40e-03 1.42e+04 3.88e+00 bond pdb=" C LEUAA 40 " pdb=" N PROAA 41 " ideal model delta sigma weight residual 1.334 1.317 0.016 8.40e-03 1.42e+04 3.86e+00 bond pdb=" C LEUAC 40 " pdb=" N PROAC 41 " ideal model delta sigma weight residual 1.334 1.318 0.016 8.40e-03 1.42e+04 3.50e+00 bond pdb=" N THRAB 13 " pdb=" CA THRAB 13 " ideal model delta sigma weight residual 1.464 1.451 0.013 9.80e-03 1.04e+04 1.77e+00 bond pdb=" C THRAB 13 " pdb=" N PROAB 14 " ideal model delta sigma weight residual 1.334 1.319 0.015 1.11e-02 8.12e+03 1.77e+00 ... (remaining 2317 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.40: 2902 1.40 - 2.81: 222 2.81 - 4.21: 32 4.21 - 5.62: 6 5.62 - 7.02: 6 Bond angle restraints: 3168 Sorted by residual: angle pdb=" C SERAA 81 " pdb=" N GLUAA 82 " pdb=" CA GLUAA 82 " ideal model delta sigma weight residual 122.42 116.68 5.74 1.55e+00 4.16e-01 1.37e+01 angle pdb=" C SERAC 81 " pdb=" N GLUAC 82 " pdb=" CA GLUAC 82 " ideal model delta sigma weight residual 122.42 116.69 5.73 1.55e+00 4.16e-01 1.37e+01 angle pdb=" C SERAB 81 " pdb=" N GLUAB 82 " pdb=" CA GLUAB 82 " ideal model delta sigma weight residual 122.42 116.72 5.70 1.55e+00 4.16e-01 1.35e+01 angle pdb=" CG1 VALAB 59 " pdb=" CB VALAB 59 " pdb=" CG2 VALAB 59 " ideal model delta sigma weight residual 110.80 103.78 7.02 2.20e+00 2.07e-01 1.02e+01 angle pdb=" CG1 VALAC 59 " pdb=" CB VALAC 59 " pdb=" CG2 VALAC 59 " ideal model delta sigma weight residual 110.80 103.78 7.02 2.20e+00 2.07e-01 1.02e+01 ... (remaining 3163 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.05: 1276 18.05 - 36.10: 83 36.10 - 54.15: 3 54.15 - 72.20: 3 72.20 - 90.25: 3 Dihedral angle restraints: 1368 sinusoidal: 507 harmonic: 861 Sorted by residual: dihedral pdb=" CA SERAB 81 " pdb=" C SERAB 81 " pdb=" N GLUAB 82 " pdb=" CA GLUAB 82 " ideal model delta harmonic sigma weight residual 180.00 160.00 20.00 0 5.00e+00 4.00e-02 1.60e+01 dihedral pdb=" CA SERAA 81 " pdb=" C SERAA 81 " pdb=" N GLUAA 82 " pdb=" CA GLUAA 82 " ideal model delta harmonic sigma weight residual 180.00 160.06 19.94 0 5.00e+00 4.00e-02 1.59e+01 dihedral pdb=" CA SERAC 81 " pdb=" C SERAC 81 " pdb=" N GLUAC 82 " pdb=" CA GLUAC 82 " ideal model delta harmonic sigma weight residual 180.00 160.11 19.89 0 5.00e+00 4.00e-02 1.58e+01 ... (remaining 1365 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 182 0.027 - 0.053: 94 0.053 - 0.080: 23 0.080 - 0.107: 34 0.107 - 0.134: 12 Chirality restraints: 345 Sorted by residual: chirality pdb=" CA VALAB 47 " pdb=" N VALAB 47 " pdb=" C VALAB 47 " pdb=" CB VALAB 47 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.46e-01 chirality pdb=" CA VALAA 47 " pdb=" N VALAA 47 " pdb=" C VALAA 47 " pdb=" CB VALAA 47 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.36e-01 chirality pdb=" CA VALAC 47 " pdb=" N VALAC 47 " pdb=" C VALAC 47 " pdb=" CB VALAC 47 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.34e-01 ... (remaining 342 not shown) Planarity restraints: 417 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLYAB 98 " 0.046 5.00e-02 4.00e+02 6.98e-02 7.81e+00 pdb=" N PROAB 99 " -0.121 5.00e-02 4.00e+02 pdb=" CA PROAB 99 " 0.036 5.00e-02 4.00e+02 pdb=" CD PROAB 99 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLYAA 98 " 0.046 5.00e-02 4.00e+02 6.96e-02 7.76e+00 pdb=" N PROAA 99 " -0.120 5.00e-02 4.00e+02 pdb=" CA PROAA 99 " 0.036 5.00e-02 4.00e+02 pdb=" CD PROAA 99 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLYAC 98 " 0.046 5.00e-02 4.00e+02 6.95e-02 7.73e+00 pdb=" N PROAC 99 " -0.120 5.00e-02 4.00e+02 pdb=" CA PROAC 99 " 0.036 5.00e-02 4.00e+02 pdb=" CD PROAC 99 " 0.038 5.00e-02 4.00e+02 ... (remaining 414 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 716 2.83 - 3.35: 1910 3.35 - 3.86: 3787 3.86 - 4.38: 4275 4.38 - 4.90: 8162 Nonbonded interactions: 18850 Sorted by model distance: nonbonded pdb=" O SERAB 68 " pdb=" OG SERAB 68 " model vdw 2.310 3.040 nonbonded pdb=" O SERAA 68 " pdb=" OG SERAA 68 " model vdw 2.310 3.040 nonbonded pdb=" O SERAC 68 " pdb=" OG SERAC 68 " model vdw 2.311 3.040 nonbonded pdb=" N GLUAA 82 " pdb=" O GLUAC 82 " model vdw 2.443 3.120 nonbonded pdb=" O GLUAA 82 " pdb=" N GLUAB 82 " model vdw 2.489 3.120 ... (remaining 18845 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: 3.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.050 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 4.540 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 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 : 0.007 0.036 2325 Z= 0.331 Angle : 0.841 7.022 3174 Z= 0.512 Chirality : 0.047 0.134 345 Planarity : 0.010 0.070 417 Dihedral : 11.863 90.251 819 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % 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: -5.51 (0.27), residues: 300 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.19 (0.20), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARGAC 58 TYR 0.015 0.002 TYRAB 88 PHE 0.005 0.002 PHEAA 101 TRP 0.005 0.001 TRPAC 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00651 / 0.33 ( 2322) covalent geometry : angle 0.84110 / 0.51 ( 3168) SS BOND : bond 0.00529 / 0.34 ( 3) SS BOND : angle 0.88597 / 0.52 ( 6) hydrogen bonds : bond 0.15960 / 11.14 ( 23) hydrogen bonds : angle 7.37504 / 4.97 ( 69) *********************** 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 49 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 0.053 Fit side-chains REVERT: AA 55 ARG cc_start: 0.7736 (ttm170) cc_final: 0.7492 (ttp-170) REVERT: AC 62 ARG cc_start: 0.6442 (ptp-170) cc_final: 0.4750 (tpm170) outliers start: 0 outliers final: 0 residues processed: 49 average time/residue: 0.0741 time to fit residues: 4.1211 Evaluate side-chains 43 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.053 ------------------------------------------------------------------------------- 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: 7.9990 chunk 12 optimal weight: 5.9990 chunk 24 optimal weight: 0.9990 chunk 28 optimal weight: 0.0980 chunk 13 optimal weight: 4.9990 chunk 1 optimal weight: 0.8980 chunk 8 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 chunk 15 optimal weight: 5.9990 chunk 29 optimal weight: 0.0980 chunk 25 optimal weight: 1.9990 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AA 35 ASN AA 80 GLN AA 106 GLN AB 35 ASN AB 80 GLN AB 106 GLN AC 80 GLN AC 106 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.141489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.120617 restraints weight = 3171.210| |-----------------------------------------------------------------------------| r_work (start): 0.3940 rms_B_bonded: 2.81 r_work: 0.3848 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.3848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.1535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 2325 Z= 0.103 Angle : 0.503 5.116 3174 Z= 0.267 Chirality : 0.042 0.120 345 Planarity : 0.008 0.070 417 Dihedral : 4.271 17.205 336 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.41 % Allowed : 10.04 % Favored : 87.55 % 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: -5.14 (0.30), residues: 300 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.91 (0.23), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARGAC 38 TYR 0.017 0.001 TYRAA 88 PHE 0.006 0.001 PHEAB 101 TRP 0.004 0.001 TRPAB 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.10 ( 2322) covalent geometry : angle 0.50282 / 0.27 ( 3168) SS BOND : bond 0.00111 / 0.07 ( 3) SS BOND : angle 0.48000 / 0.31 ( 6) hydrogen bonds : bond 0.02473 / 1.81 ( 23) hydrogen bonds : angle 5.63135 / 3.94 ( 69) *********************** 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 49 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 43 time to evaluate : 0.061 Fit side-chains REVERT: AC 62 ARG cc_start: 0.6454 (ptp-170) cc_final: 0.4688 (tpm170) REVERT: AC 82 GLU cc_start: 0.7150 (mm-30) cc_final: 0.6833 (tt0) outliers start: 6 outliers final: 4 residues processed: 45 average time/residue: 0.0777 time to fit residues: 3.9728 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 : 0.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AA residue 13 THR Chi-restraints excluded: chain AA residue 82 GLU Chi-restraints excluded: chain AB residue 13 THR Chi-restraints excluded: chain AC residue 13 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 16 optimal weight: 8.9990 chunk 14 optimal weight: 4.9990 chunk 29 optimal weight: 4.9990 chunk 18 optimal weight: 4.9990 chunk 26 optimal weight: 0.4980 chunk 19 optimal weight: 5.9990 chunk 7 optimal weight: 9.9990 chunk 21 optimal weight: 2.9990 chunk 12 optimal weight: 0.0870 chunk 9 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 overall best weight: 1.3164 ------------------------------------------------------------------------------- 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 = 0.4119 r_free = 0.4119 target = 0.138197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.117262 restraints weight = 3265.402| |-----------------------------------------------------------------------------| r_work (start): 0.3894 rms_B_bonded: 2.88 r_work: 0.3805 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.1686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 2325 Z= 0.140 Angle : 0.502 5.318 3174 Z= 0.267 Chirality : 0.042 0.123 345 Planarity : 0.007 0.061 417 Dihedral : 4.203 17.564 336 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 1.20 % Allowed : 10.84 % Favored : 87.95 % 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: -4.89 (0.32), residues: 300 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.72 (0.25), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARGAC 38 TYR 0.019 0.002 TYRAA 88 PHE 0.005 0.001 PHEAB 101 TRP 0.005 0.001 TRPAB 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.14 ( 2322) covalent geometry : angle 0.50160 / 0.27 ( 3168) SS BOND : bond 0.00278 / 0.17 ( 3) SS BOND : angle 0.55581 / 0.33 ( 6) hydrogen bonds : bond 0.02188 / 1.58 ( 23) hydrogen bonds : angle 5.16942 / 3.57 ( 69) *********************** 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 42 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 39 time to evaluate : 0.092 Fit side-chains REVERT: AC 62 ARG cc_start: 0.6398 (ptp-170) cc_final: 0.4570 (tpm170) REVERT: AC 82 GLU cc_start: 0.7424 (mm-30) cc_final: 0.6959 (mp0) outliers start: 3 outliers final: 3 residues processed: 39 average time/residue: 0.0852 time to fit residues: 3.8084 Evaluate side-chains 42 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 39 time to evaluate : 0.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AA residue 13 THR Chi-restraints excluded: chain AB residue 13 THR Chi-restraints excluded: chain AC residue 13 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 9 optimal weight: 1.9990 chunk 11 optimal weight: 6.9990 chunk 29 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 chunk 28 optimal weight: 0.8980 chunk 14 optimal weight: 0.5980 chunk 1 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 3 optimal weight: 0.8980 chunk 19 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AA 80 GLN AB 80 GLN AC 80 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.141305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.120577 restraints weight = 3186.829| |-----------------------------------------------------------------------------| r_work (start): 0.3946 rms_B_bonded: 2.83 r_work: 0.3858 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.3858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.1909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 2325 Z= 0.107 Angle : 0.474 4.962 3174 Z= 0.250 Chirality : 0.042 0.119 345 Planarity : 0.007 0.064 417 Dihedral : 3.920 16.860 336 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 2.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 2.01 % Allowed : 12.05 % Favored : 85.94 % 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: -4.70 (0.34), residues: 300 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.57 (0.26), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARGAC 38 TYR 0.018 0.002 TYRAA 88 PHE 0.005 0.001 PHEAB 101 TRP 0.004 0.001 TRPAA 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.11 ( 2322) covalent geometry : angle 0.47413 / 0.25 ( 3168) SS BOND : bond 0.00175 / 0.11 ( 3) SS BOND : angle 0.39965 / 0.24 ( 6) hydrogen bonds : bond 0.01977 / 1.39 ( 23) hydrogen bonds : angle 4.98935 / 3.45 ( 69) *********************** 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: 5 poor density : 39 time to evaluate : 0.068 Fit side-chains REVERT: AA 62 ARG cc_start: 0.6783 (ptm-80) cc_final: 0.6539 (ptm-80) REVERT: AC 62 ARG cc_start: 0.6400 (ptp-170) cc_final: 0.4604 (tpm170) REVERT: AC 82 GLU cc_start: 0.7393 (mm-30) cc_final: 0.7153 (tt0) outliers start: 5 outliers final: 5 residues processed: 39 average time/residue: 0.0730 time to fit residues: 3.2107 Evaluate side-chains 44 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 39 time to evaluate : 0.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AA residue 13 THR Chi-restraints excluded: chain AA residue 61 ASP Chi-restraints excluded: chain AB residue 13 THR Chi-restraints excluded: chain AC residue 13 THR Chi-restraints excluded: chain AC residue 64 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 4 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 22 optimal weight: 0.2980 chunk 15 optimal weight: 0.0000 chunk 28 optimal weight: 3.9990 chunk 11 optimal weight: 7.9990 chunk 2 optimal weight: 0.9980 chunk 8 optimal weight: 0.6980 chunk 20 optimal weight: 10.0000 chunk 18 optimal weight: 4.9990 chunk 6 optimal weight: 0.9980 overall best weight: 0.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AC 80 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.144523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.123667 restraints weight = 3165.525| |-----------------------------------------------------------------------------| r_work (start): 0.3999 rms_B_bonded: 2.85 r_work: 0.3909 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.3909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.2214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 2325 Z= 0.092 Angle : 0.458 4.802 3174 Z= 0.240 Chirality : 0.041 0.123 345 Planarity : 0.007 0.060 417 Dihedral : 3.660 15.474 336 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 1.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 1.20 % Allowed : 14.46 % Favored : 84.34 % 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: -4.60 (0.35), residues: 300 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.50 (0.27), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARGAB 58 TYR 0.014 0.001 TYRAA 88 PHE 0.007 0.001 PHEAB 101 TRP 0.003 0.001 TRPAB 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.09 ( 2322) covalent geometry : angle 0.45773 / 0.24 ( 3168) SS BOND : bond 0.00120 / 0.07 ( 3) SS BOND : angle 0.32943 / 0.20 ( 6) hydrogen bonds : bond 0.01805 / 1.25 ( 23) hydrogen bonds : angle 4.78900 / 3.32 ( 69) *********************** 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 45 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 42 time to evaluate : 0.090 Fit side-chains REVERT: AA 62 ARG cc_start: 0.6776 (ptm-80) cc_final: 0.6519 (ptm-80) REVERT: AC 62 ARG cc_start: 0.6432 (ptp-170) cc_final: 0.4630 (tpm170) REVERT: AC 82 GLU cc_start: 0.7333 (mm-30) cc_final: 0.7127 (tt0) outliers start: 3 outliers final: 3 residues processed: 42 average time/residue: 0.0685 time to fit residues: 3.2947 Evaluate side-chains 43 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 40 time to evaluate : 0.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AA residue 13 THR Chi-restraints excluded: chain AB residue 13 THR Chi-restraints excluded: chain AC residue 13 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 13 optimal weight: 7.9990 chunk 4 optimal weight: 3.9990 chunk 9 optimal weight: 0.9990 chunk 1 optimal weight: 9.9990 chunk 3 optimal weight: 2.9990 chunk 26 optimal weight: 6.9990 chunk 25 optimal weight: 1.9990 chunk 27 optimal weight: 7.9990 chunk 14 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 8 optimal weight: 0.8980 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AA 80 GLN AB 80 GLN AC 80 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.136753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.115843 restraints weight = 3280.201| |-----------------------------------------------------------------------------| r_work (start): 0.3879 rms_B_bonded: 2.86 r_work: 0.3786 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.3786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.1980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 2325 Z= 0.169 Angle : 0.505 5.016 3174 Z= 0.270 Chirality : 0.042 0.127 345 Planarity : 0.007 0.061 417 Dihedral : 4.108 16.570 336 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 2.01 % Allowed : 14.86 % Favored : 83.13 % 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: -4.59 (0.35), residues: 300 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.49 (0.26), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARGAB 55 TYR 0.019 0.002 TYRAA 88 PHE 0.004 0.001 PHEAB 63 TRP 0.007 0.001 TRPAA 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.17 ( 2322) covalent geometry : angle 0.50483 / 0.27 ( 3168) SS BOND : bond 0.00356 / 0.21 ( 3) SS BOND : angle 0.61659 / 0.35 ( 6) hydrogen bonds : bond 0.02174 / 1.49 ( 23) hydrogen bonds : angle 4.72061 / 3.31 ( 69) *********************** 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 42 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 37 time to evaluate : 0.054 Fit side-chains REVERT: AC 62 ARG cc_start: 0.6426 (ptp-170) cc_final: 0.4538 (tpm170) REVERT: AC 82 GLU cc_start: 0.7532 (mm-30) cc_final: 0.7217 (mp0) outliers start: 5 outliers final: 4 residues processed: 38 average time/residue: 0.0788 time to fit residues: 3.4427 Evaluate side-chains 41 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 37 time to evaluate : 0.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AA residue 13 THR Chi-restraints excluded: chain AB residue 13 THR Chi-restraints excluded: chain AC residue 13 THR Chi-restraints excluded: chain AC residue 39 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 21 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 chunk 4 optimal weight: 4.9990 chunk 20 optimal weight: 0.0070 chunk 19 optimal weight: 0.0050 chunk 22 optimal weight: 5.9990 chunk 16 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 chunk 26 optimal weight: 5.9990 overall best weight: 1.2016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AC 80 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.139343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.118463 restraints weight = 3235.273| |-----------------------------------------------------------------------------| r_work (start): 0.3923 rms_B_bonded: 2.86 r_work: 0.3829 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.3829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.2113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 2325 Z= 0.128 Angle : 0.483 4.770 3174 Z= 0.256 Chirality : 0.042 0.126 345 Planarity : 0.007 0.062 417 Dihedral : 3.944 16.771 336 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 2.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 1.61 % Allowed : 15.26 % Favored : 83.13 % 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: -4.53 (0.35), residues: 300 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.45 (0.27), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARGAA 38 TYR 0.020 0.002 TYRAA 88 PHE 0.004 0.001 PHEAB 101 TRP 0.004 0.001 TRPAA 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.13 ( 2322) covalent geometry : angle 0.48260 / 0.26 ( 3168) SS BOND : bond 0.00240 / 0.15 ( 3) SS BOND : angle 0.49326 / 0.29 ( 6) hydrogen bonds : bond 0.02055 / 1.41 ( 23) hydrogen bonds : angle 4.69226 / 3.28 ( 69) *********************** 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 43 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 39 time to evaluate : 0.094 Fit side-chains REVERT: AA 62 ARG cc_start: 0.6769 (ptm-80) cc_final: 0.6546 (ptm-80) REVERT: AC 62 ARG cc_start: 0.6413 (ptp-170) cc_final: 0.4534 (tpm170) outliers start: 4 outliers final: 4 residues processed: 39 average time/residue: 0.0771 time to fit residues: 3.4672 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 : 0.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AA residue 13 THR Chi-restraints excluded: chain AB residue 13 THR Chi-restraints excluded: chain AC residue 13 THR Chi-restraints excluded: chain AC residue 61 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 8 optimal weight: 4.9990 chunk 6 optimal weight: 5.9990 chunk 5 optimal weight: 0.9980 chunk 17 optimal weight: 5.9990 chunk 25 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 21 optimal weight: 4.9990 chunk 9 optimal weight: 0.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AA 80 GLN AC 80 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.138648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.118231 restraints weight = 3229.743| |-----------------------------------------------------------------------------| r_work (start): 0.3917 rms_B_bonded: 2.83 r_work: 0.3826 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work (final): 0.3826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.2215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 2325 Z= 0.140 Angle : 0.489 5.231 3174 Z= 0.260 Chirality : 0.042 0.127 345 Planarity : 0.007 0.061 417 Dihedral : 3.997 16.107 336 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 2.01 % Allowed : 15.26 % Favored : 82.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.54 (0.35), residues: 300 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.46 (0.27), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARGAB 38 TYR 0.021 0.002 TYRAA 88 PHE 0.004 0.001 PHEAB 101 TRP 0.005 0.001 TRPAC 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.14 ( 2322) covalent geometry : angle 0.48911 / 0.26 ( 3168) SS BOND : bond 0.00275 / 0.17 ( 3) SS BOND : angle 0.56355 / 0.33 ( 6) hydrogen bonds : bond 0.02083 / 1.43 ( 23) hydrogen bonds : angle 4.66465 / 3.26 ( 69) *********************** 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 40 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 35 time to evaluate : 0.084 Fit side-chains REVERT: AA 62 ARG cc_start: 0.6785 (ptm-80) cc_final: 0.6544 (ptm-80) REVERT: AC 62 ARG cc_start: 0.6392 (ptp-170) cc_final: 0.4505 (tpm170) outliers start: 5 outliers final: 5 residues processed: 37 average time/residue: 0.0807 time to fit residues: 3.4421 Evaluate side-chains 40 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 35 time to evaluate : 0.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AA residue 13 THR Chi-restraints excluded: chain AB residue 13 THR Chi-restraints excluded: chain AC residue 13 THR Chi-restraints excluded: chain AC residue 39 GLN Chi-restraints excluded: chain AC residue 61 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 14 optimal weight: 1.9990 chunk 16 optimal weight: 6.9990 chunk 29 optimal weight: 4.9990 chunk 23 optimal weight: 9.9990 chunk 5 optimal weight: 9.9990 chunk 1 optimal weight: 4.9990 chunk 28 optimal weight: 0.8980 chunk 9 optimal weight: 0.8980 chunk 7 optimal weight: 7.9990 chunk 10 optimal weight: 0.4980 chunk 6 optimal weight: 0.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AC 80 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.140163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.120003 restraints weight = 3243.173| |-----------------------------------------------------------------------------| r_work (start): 0.3942 rms_B_bonded: 2.83 r_work: 0.3849 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work (final): 0.3849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.2323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 2325 Z= 0.118 Angle : 0.477 5.257 3174 Z= 0.252 Chirality : 0.042 0.132 345 Planarity : 0.007 0.062 417 Dihedral : 3.852 15.926 336 Min Nonbonded Distance : 2.646 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 2.01 % Allowed : 15.66 % Favored : 82.33 % 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: -4.52 (0.36), residues: 300 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.44 (0.27), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARGAB 38 TYR 0.020 0.002 TYRAA 88 PHE 0.005 0.001 PHEAB 101 TRP 0.004 0.001 TRPAC 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.12 ( 2322) covalent geometry : angle 0.47710 / 0.25 ( 3168) SS BOND : bond 0.00197 / 0.12 ( 3) SS BOND : angle 0.45065 / 0.27 ( 6) hydrogen bonds : bond 0.01992 / 1.36 ( 23) hydrogen bonds : angle 4.60346 / 3.21 ( 69) *********************** 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 44 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 39 time to evaluate : 0.090 Fit side-chains REVERT: AA 62 ARG cc_start: 0.6780 (ptm-80) cc_final: 0.6532 (ptm-80) REVERT: AC 62 ARG cc_start: 0.6403 (ptp-170) cc_final: 0.4516 (tpm170) outliers start: 5 outliers final: 5 residues processed: 41 average time/residue: 0.0818 time to fit residues: 3.8526 Evaluate side-chains 42 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 37 time to evaluate : 0.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AA residue 13 THR Chi-restraints excluded: chain AB residue 13 THR Chi-restraints excluded: chain AC residue 13 THR Chi-restraints excluded: chain AC residue 39 GLN Chi-restraints excluded: chain AC residue 61 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 17 optimal weight: 7.9990 chunk 15 optimal weight: 9.9990 chunk 14 optimal weight: 6.9990 chunk 18 optimal weight: 3.9990 chunk 6 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 chunk 19 optimal weight: 0.4980 chunk 2 optimal weight: 0.9990 chunk 3 optimal weight: 2.9990 chunk 21 optimal weight: 5.9990 chunk 8 optimal weight: 0.9990 overall best weight: 1.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AA 80 GLN AC 80 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.139187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.119710 restraints weight = 3259.524| |-----------------------------------------------------------------------------| r_work (start): 0.3897 rms_B_bonded: 2.67 r_work: 0.3798 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3679 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.2279 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= 0.163 Angle : 0.505 5.431 3174 Z= 0.269 Chirality : 0.043 0.135 345 Planarity : 0.007 0.059 417 Dihedral : 4.048 15.929 336 Min Nonbonded Distance : 2.646 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 2.01 % Allowed : 16.06 % Favored : 81.93 % 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: -4.57 (0.36), residues: 300 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.47 (0.27), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARGAB 38 TYR 0.025 0.002 TYRAA 88 PHE 0.004 0.001 PHEAB 101 TRP 0.006 0.001 TRPAC 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.16 ( 2322) covalent geometry : angle 0.50456 / 0.27 ( 3168) SS BOND : bond 0.00336 / 0.20 ( 3) SS BOND : angle 0.66088 / 0.38 ( 6) hydrogen bonds : bond 0.02116 / 1.46 ( 23) hydrogen bonds : angle 4.65628 / 3.25 ( 69) ********************** 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 41 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 36 time to evaluate : 0.090 Fit side-chains REVERT: AA 62 ARG cc_start: 0.7030 (ptm-80) cc_final: 0.6772 (ptm-80) REVERT: AC 62 ARG cc_start: 0.6638 (ptp-170) cc_final: 0.4640 (tpm170) outliers start: 5 outliers final: 5 residues processed: 38 average time/residue: 0.0833 time to fit residues: 3.6996 Evaluate side-chains 41 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 36 time to evaluate : 0.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AA residue 13 THR Chi-restraints excluded: chain AB residue 13 THR Chi-restraints excluded: chain AC residue 13 THR Chi-restraints excluded: chain AC residue 39 GLN Chi-restraints excluded: chain AC residue 61 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 18 optimal weight: 3.9990 chunk 28 optimal weight: 0.4980 chunk 14 optimal weight: 6.9990 chunk 7 optimal weight: 10.0000 chunk 22 optimal weight: 0.0170 chunk 21 optimal weight: 2.9990 chunk 19 optimal weight: 5.9990 chunk 27 optimal weight: 0.0270 chunk 29 optimal weight: 0.8980 chunk 11 optimal weight: 5.9990 chunk 9 optimal weight: 0.6980 overall best weight: 0.4276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AC 80 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.142418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.123542 restraints weight = 3319.678| |-----------------------------------------------------------------------------| r_work (start): 0.3980 rms_B_bonded: 2.74 r_work: 0.3882 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3772 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.2590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 2325 Z= 0.088 Angle : 0.463 5.329 3174 Z= 0.241 Chirality : 0.042 0.131 345 Planarity : 0.007 0.063 417 Dihedral : 3.533 14.604 336 Min Nonbonded Distance : 2.650 Molprobity Statistics. All-atom Clashscore : 2.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 1.61 % Allowed : 16.06 % Favored : 82.33 % 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: -4.48 (0.36), residues: 300 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.40 (0.27), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARGAA 38 TYR 0.016 0.001 TYRAA 88 PHE 0.008 0.001 PHEAB 101 TRP 0.003 0.001 TRPAB 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.09 ( 2322) covalent geometry : angle 0.46324 / 0.24 ( 3168) SS BOND : bond 0.00047 / 0.03 ( 3) SS BOND : angle 0.27988 / 0.18 ( 6) hydrogen bonds : bond 0.01907 / 1.32 ( 23) hydrogen bonds : angle 4.56475 / 3.16 ( 69) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 819.31 seconds wall clock time: 14 minutes 46.52 seconds (886.52 seconds total)