Starting phenix.real_space_refine on Tue Feb 3 12:33:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9k8g_62172/02_2026/9k8g_62172.cif Found real_map, /net/cci-nas-00/data/ceres_data/9k8g_62172/02_2026/9k8g_62172.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9k8g_62172/02_2026/9k8g_62172.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9k8g_62172/02_2026/9k8g_62172.map" model { file = "/net/cci-nas-00/data/ceres_data/9k8g_62172/02_2026/9k8g_62172.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9k8g_62172/02_2026/9k8g_62172.cif" } resolution = 2.75 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= 0.002 sd= 0.234 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: 5 Type Number sf(0) Gaussians Zn 3 6.06 5 S 6 5.16 5 C 1353 2.51 5 N 351 2.21 5 O 375 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 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: 2088 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 695 Classifications: {'peptide': 86} Link IDs: {'TRANS': 85} Chain: "B" Number of atoms: 695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 695 Classifications: {'peptide': 86} Link IDs: {'TRANS': 85} Chain: "C" Number of atoms: 695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 695 Classifications: {'peptide': 86} Link IDs: {'TRANS': 85} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 0.43, per 1000 atoms: 0.21 Number of scatterers: 2088 At special positions: 0 Unit cell: (67.8699, 64.638, 42.0147, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 3 29.99 S 6 16.00 O 375 8.00 N 351 7.00 C 1353 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.12 Conformation dependent library (CDL) restraints added in 48.6 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 301 " pdb="ZN ZN A 301 " - pdb=" NE2 HIS A 47 " pdb="ZN ZN A 301 " - pdb=" NE2 HIS B 36 " pdb=" ZN B 301 " pdb="ZN ZN B 301 " - pdb=" NE2 HIS C 36 " pdb="ZN ZN B 301 " - pdb=" NE2 HIS B 47 " pdb=" ZN C 301 " pdb="ZN ZN C 301 " - pdb=" NE2 HIS A 36 " pdb="ZN ZN C 301 " - pdb=" NE2 HIS C 47 " 504 Ramachandran restraints generated. 252 Oldfield, 0 Emsley, 252 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 480 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 0 sheets defined 91.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.04 Creating SS restraints... Processing helix chain 'A' and resid 5 through 23 Processing helix chain 'A' and resid 26 through 41 Processing helix chain 'A' and resid 43 through 56 removed outlier: 3.551A pdb=" N HIS A 47 " --> pdb=" O LEU A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 59 through 75 Processing helix chain 'A' and resid 76 through 90 Processing helix chain 'B' and resid 6 through 23 Processing helix chain 'B' and resid 26 through 40 Processing helix chain 'B' and resid 43 through 56 Processing helix chain 'B' and resid 59 through 73 removed outlier: 3.700A pdb=" N LYS B 73 " --> pdb=" O GLU B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 90 Processing helix chain 'C' and resid 6 through 22 Processing helix chain 'C' and resid 26 through 41 Processing helix chain 'C' and resid 43 through 56 removed outlier: 3.671A pdb=" N HIS C 47 " --> pdb=" O LEU C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 59 through 75 Processing helix chain 'C' and resid 76 through 90 removed outlier: 3.627A pdb=" N PHE C 81 " --> pdb=" O ASP C 77 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N VAL C 82 " --> pdb=" O ASP C 78 " (cutoff:3.500A) 172 hydrogen bonds defined for protein. 516 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: 0.18 Time building geometry restraints manager: 0.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 696 1.35 - 1.46: 425 1.46 - 1.58: 976 1.58 - 1.70: 0 1.70 - 1.82: 12 Bond restraints: 2109 Sorted by residual: bond pdb=" CB GLU B 7 " pdb=" CG GLU B 7 " ideal model delta sigma weight residual 1.520 1.550 -0.030 3.00e-02 1.11e+03 9.88e-01 bond pdb=" N VAL B 72 " pdb=" CA VAL B 72 " ideal model delta sigma weight residual 1.461 1.454 0.007 1.19e-02 7.06e+03 3.22e-01 bond pdb=" CB ARG B 66 " pdb=" CG ARG B 66 " ideal model delta sigma weight residual 1.520 1.504 0.016 3.00e-02 1.11e+03 2.94e-01 bond pdb=" CB MET C 6 " pdb=" CG MET C 6 " ideal model delta sigma weight residual 1.520 1.536 -0.016 3.00e-02 1.11e+03 2.90e-01 bond pdb=" CB ARG A 19 " pdb=" CG ARG A 19 " ideal model delta sigma weight residual 1.520 1.504 0.016 3.00e-02 1.11e+03 2.74e-01 ... (remaining 2104 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.20: 2743 1.20 - 2.40: 76 2.40 - 3.59: 7 3.59 - 4.79: 5 4.79 - 5.99: 1 Bond angle restraints: 2832 Sorted by residual: angle pdb=" N GLU C 27 " pdb=" CA GLU C 27 " pdb=" C GLU C 27 " ideal model delta sigma weight residual 111.36 113.75 -2.39 1.09e+00 8.42e-01 4.79e+00 angle pdb=" N GLU A 27 " pdb=" CA GLU A 27 " pdb=" C GLU A 27 " ideal model delta sigma weight residual 111.28 113.63 -2.35 1.09e+00 8.42e-01 4.64e+00 angle pdb=" CA GLU B 7 " pdb=" CB GLU B 7 " pdb=" CG GLU B 7 " ideal model delta sigma weight residual 114.10 118.22 -4.12 2.00e+00 2.50e-01 4.25e+00 angle pdb=" N ASP C 77 " pdb=" CA ASP C 77 " pdb=" C ASP C 77 " ideal model delta sigma weight residual 111.28 113.46 -2.18 1.09e+00 8.42e-01 3.99e+00 angle pdb=" CB MET C 6 " pdb=" CG MET C 6 " pdb=" SD MET C 6 " ideal model delta sigma weight residual 112.70 118.69 -5.99 3.00e+00 1.11e-01 3.98e+00 ... (remaining 2827 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.90: 1023 15.90 - 31.80: 165 31.80 - 47.71: 61 47.71 - 63.61: 26 63.61 - 79.51: 3 Dihedral angle restraints: 1278 sinusoidal: 534 harmonic: 744 Sorted by residual: dihedral pdb=" CG ARG C 39 " pdb=" CD ARG C 39 " pdb=" NE ARG C 39 " pdb=" CZ ARG C 39 " ideal model delta sinusoidal sigma weight residual -90.00 -39.86 -50.14 2 1.50e+01 4.44e-03 1.26e+01 dihedral pdb=" CG ARG C 52 " pdb=" CD ARG C 52 " pdb=" NE ARG C 52 " pdb=" CZ ARG C 52 " ideal model delta sinusoidal sigma weight residual 90.00 133.70 -43.70 2 1.50e+01 4.44e-03 1.02e+01 dihedral pdb=" CB MET B 6 " pdb=" CG MET B 6 " pdb=" SD MET B 6 " pdb=" CE MET B 6 " ideal model delta sinusoidal sigma weight residual 60.00 119.51 -59.51 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 1275 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 179 0.024 - 0.048: 93 0.048 - 0.072: 46 0.072 - 0.096: 12 0.096 - 0.120: 3 Chirality restraints: 333 Sorted by residual: chirality pdb=" CA ILE B 58 " pdb=" N ILE B 58 " pdb=" C ILE B 58 " pdb=" CB ILE B 58 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.58e-01 chirality pdb=" CA ILE A 58 " pdb=" N ILE A 58 " pdb=" C ILE A 58 " pdb=" CB ILE A 58 " both_signs ideal model delta sigma weight residual False 2.43 2.54 -0.11 2.00e-01 2.50e+01 2.96e-01 chirality pdb=" CA ILE C 58 " pdb=" N ILE C 58 " pdb=" C ILE C 58 " pdb=" CB ILE C 58 " both_signs ideal model delta sigma weight residual False 2.43 2.53 -0.10 2.00e-01 2.50e+01 2.44e-01 ... (remaining 330 not shown) Planarity restraints: 357 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 39 " 0.050 9.50e-02 1.11e+02 2.33e-02 7.29e-01 pdb=" NE ARG C 39 " -0.007 2.00e-02 2.50e+03 pdb=" CZ ARG C 39 " 0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG C 39 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG C 39 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 68 " 0.005 2.00e-02 2.50e+03 3.44e-03 2.37e-01 pdb=" CG TYR A 68 " -0.008 2.00e-02 2.50e+03 pdb=" CD1 TYR A 68 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR A 68 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR A 68 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR A 68 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR A 68 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR A 68 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG C 11 " -0.002 2.00e-02 2.50e+03 4.46e-03 1.99e-01 pdb=" C ARG C 11 " 0.008 2.00e-02 2.50e+03 pdb=" O ARG C 11 " -0.003 2.00e-02 2.50e+03 pdb=" N ARG C 12 " -0.003 2.00e-02 2.50e+03 ... (remaining 354 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 17 2.58 - 3.16: 1590 3.16 - 3.74: 3213 3.74 - 4.32: 4603 4.32 - 4.90: 7580 Nonbonded interactions: 17003 Sorted by model distance: nonbonded pdb=" OD2 ASP A 51 " pdb="ZN ZN A 301 " model vdw 2.002 2.230 nonbonded pdb=" OD2 ASP B 51 " pdb="ZN ZN B 301 " model vdw 2.033 2.230 nonbonded pdb=" OD2 ASP B 40 " pdb="ZN ZN A 301 " model vdw 2.045 2.230 nonbonded pdb=" OD2 ASP A 40 " pdb="ZN ZN C 301 " model vdw 2.048 2.230 nonbonded pdb=" OD2 ASP C 40 " pdb="ZN ZN B 301 " model vdw 2.058 2.230 ... (remaining 16998 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 'A' selection = chain 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.030 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 3.050 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 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 : 0.010 0.204 2115 Z= 0.331 Angle : 0.509 5.988 2832 Z= 0.310 Chirality : 0.036 0.120 333 Planarity : 0.002 0.023 357 Dihedral : 19.204 79.512 798 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.93 % Allowed : 29.63 % Favored : 69.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.95 (0.50), residues: 252 helix: 2.12 (0.32), residues: 237 sheet: None (None), residues: 0 loop : -0.72 (0.80), residues: 15 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 39 TYR 0.008 0.002 TYR A 68 PHE 0.005 0.001 PHE A 88 HIS 0.001 0.001 HIS C 36 Details of bonding type rmsd covalent geometry : bond 0.00264 ( 2109) covalent geometry : angle 0.50866 ( 2832) hydrogen bonds : bond 0.14417 ( 172) hydrogen bonds : angle 4.46689 ( 516) metal coordination : bond 0.17149 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 504 Ramachandran restraints generated. 252 Oldfield, 0 Emsley, 252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 504 Ramachandran restraints generated. 252 Oldfield, 0 Emsley, 252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 52 time to evaluate : 0.052 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 53 average time/residue: 0.7336 time to fit residues: 39.2718 Evaluate side-chains 55 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 54 time to evaluate : 0.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 12 optimal weight: 0.9980 chunk 13 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 16 optimal weight: 0.8980 chunk 15 optimal weight: 0.9990 chunk 9 optimal weight: 0.7980 chunk 11 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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 = 0.3693 r_free = 0.3693 target = 0.155644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.138952 restraints weight = 1755.301| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 1.11 r_work: 0.3424 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3284 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.0912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 2115 Z= 0.143 Angle : 0.457 5.168 2832 Z= 0.243 Chirality : 0.036 0.106 333 Planarity : 0.003 0.029 357 Dihedral : 4.788 55.652 288 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 3.70 % Allowed : 27.31 % Favored : 68.98 % 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: 3.59 (0.50), residues: 252 helix: 2.53 (0.32), residues: 237 sheet: None (None), residues: 0 loop : -0.58 (1.03), residues: 15 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 39 TYR 0.008 0.002 TYR C 20 PHE 0.006 0.001 PHE A 88 HIS 0.002 0.001 HIS A 47 Details of bonding type rmsd covalent geometry : bond 0.00323 ( 2109) covalent geometry : angle 0.45693 ( 2832) hydrogen bonds : bond 0.05285 ( 172) hydrogen bonds : angle 3.68286 ( 516) metal coordination : bond 0.00251 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 504 Ramachandran restraints generated. 252 Oldfield, 0 Emsley, 252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 504 Ramachandran restraints generated. 252 Oldfield, 0 Emsley, 252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 56 time to evaluate : 0.083 Fit side-chains REVERT: B 48 GLU cc_start: 0.8025 (mt-10) cc_final: 0.7734 (mt-10) outliers start: 8 outliers final: 4 residues processed: 57 average time/residue: 0.7114 time to fit residues: 41.0097 Evaluate side-chains 56 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 52 time to evaluate : 0.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 63 MET Chi-restraints excluded: chain C residue 78 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 14 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 chunk 18 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 15 optimal weight: 0.0980 chunk 7 optimal weight: 0.5980 chunk 5 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 2 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 47 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.157812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.140971 restraints weight = 1774.694| |-----------------------------------------------------------------------------| r_work (start): 0.3572 rms_B_bonded: 1.12 r_work: 0.3450 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3312 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.1057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.310 2115 Z= 0.253 Angle : 0.414 4.887 2832 Z= 0.220 Chirality : 0.034 0.108 333 Planarity : 0.003 0.033 357 Dihedral : 3.272 10.894 285 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.31 % Allowed : 28.24 % Favored : 69.44 % 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: 4.05 (0.50), residues: 252 helix: 2.82 (0.32), residues: 237 sheet: None (None), residues: 0 loop : -0.22 (1.05), residues: 15 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 39 TYR 0.007 0.002 TYR C 20 PHE 0.005 0.001 PHE A 88 HIS 0.001 0.000 HIS C 36 Details of bonding type rmsd covalent geometry : bond 0.00244 ( 2109) covalent geometry : angle 0.41409 ( 2832) hydrogen bonds : bond 0.04593 ( 172) hydrogen bonds : angle 3.45089 ( 516) metal coordination : bond 0.12648 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 504 Ramachandran restraints generated. 252 Oldfield, 0 Emsley, 252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 504 Ramachandran restraints generated. 252 Oldfield, 0 Emsley, 252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 53 time to evaluate : 0.049 Fit side-chains REVERT: B 48 GLU cc_start: 0.8043 (mt-10) cc_final: 0.7824 (mt-10) REVERT: C 39 ARG cc_start: 0.8078 (ttm-80) cc_final: 0.7580 (tpp-160) outliers start: 5 outliers final: 4 residues processed: 53 average time/residue: 0.6350 time to fit residues: 34.0299 Evaluate side-chains 56 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 52 time to evaluate : 0.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 63 MET Chi-restraints excluded: chain C residue 78 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 18 optimal weight: 0.9990 chunk 4 optimal weight: 0.8980 chunk 0 optimal weight: 6.9990 chunk 23 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 3 optimal weight: 0.7980 chunk 2 optimal weight: 0.9990 chunk 22 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 21 optimal weight: 0.7980 chunk 6 optimal weight: 0.6980 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 = 0.3698 r_free = 0.3698 target = 0.155963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.139170 restraints weight = 1745.835| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 1.14 r_work: 0.3388 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3247 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.1120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 2115 Z= 0.136 Angle : 0.444 5.787 2832 Z= 0.233 Chirality : 0.035 0.107 333 Planarity : 0.002 0.021 357 Dihedral : 3.304 10.645 285 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 3.70 % Allowed : 26.85 % Favored : 69.44 % 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: 4.00 (0.49), residues: 252 helix: 2.80 (0.32), residues: 237 sheet: None (None), residues: 0 loop : -0.50 (1.01), residues: 15 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 39 TYR 0.009 0.002 TYR C 20 PHE 0.006 0.001 PHE A 88 HIS 0.001 0.001 HIS C 36 Details of bonding type rmsd covalent geometry : bond 0.00304 ( 2109) covalent geometry : angle 0.44373 ( 2832) hydrogen bonds : bond 0.05043 ( 172) hydrogen bonds : angle 3.50496 ( 516) metal coordination : bond 0.00256 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 504 Ramachandran restraints generated. 252 Oldfield, 0 Emsley, 252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 504 Ramachandran restraints generated. 252 Oldfield, 0 Emsley, 252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 58 time to evaluate : 0.081 Fit side-chains REVERT: B 7 GLU cc_start: 0.7158 (mp0) cc_final: 0.6871 (tt0) REVERT: B 48 GLU cc_start: 0.8145 (mt-10) cc_final: 0.7856 (mt-10) outliers start: 8 outliers final: 7 residues processed: 58 average time/residue: 0.9081 time to fit residues: 53.2117 Evaluate side-chains 60 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 53 time to evaluate : 0.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 63 MET Chi-restraints excluded: chain B residue 89 LYS Chi-restraints excluded: chain C residue 78 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 21 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 22 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 20 optimal weight: 0.9980 chunk 16 optimal weight: 0.7980 chunk 18 optimal weight: 0.3980 chunk 17 optimal weight: 0.9980 chunk 1 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3705 r_free = 0.3705 target = 0.156559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.139772 restraints weight = 1752.033| |-----------------------------------------------------------------------------| r_work (start): 0.3539 rms_B_bonded: 1.14 r_work: 0.3412 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3272 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.1186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.015 2115 Z= 0.126 Angle : 0.423 4.819 2832 Z= 0.225 Chirality : 0.035 0.107 333 Planarity : 0.003 0.030 357 Dihedral : 3.278 10.481 285 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 4.63 % Allowed : 25.46 % Favored : 69.91 % 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: 4.14 (0.49), residues: 252 helix: 2.89 (0.31), residues: 237 sheet: None (None), residues: 0 loop : -0.44 (1.06), residues: 15 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 39 TYR 0.008 0.002 TYR C 20 PHE 0.006 0.001 PHE A 88 HIS 0.001 0.000 HIS C 36 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 2109) covalent geometry : angle 0.42307 ( 2832) hydrogen bonds : bond 0.04838 ( 172) hydrogen bonds : angle 3.45854 ( 516) metal coordination : bond 0.00239 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 504 Ramachandran restraints generated. 252 Oldfield, 0 Emsley, 252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 504 Ramachandran restraints generated. 252 Oldfield, 0 Emsley, 252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 53 time to evaluate : 0.052 Fit side-chains REVERT: B 39 ARG cc_start: 0.8077 (OUTLIER) cc_final: 0.6870 (ttp-170) REVERT: B 48 GLU cc_start: 0.8152 (mt-10) cc_final: 0.7889 (mt-10) REVERT: C 39 ARG cc_start: 0.8230 (ttm-80) cc_final: 0.7735 (tpp-160) outliers start: 10 outliers final: 6 residues processed: 54 average time/residue: 0.9690 time to fit residues: 52.8680 Evaluate side-chains 58 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 51 time to evaluate : 0.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 39 ARG Chi-restraints excluded: chain B residue 63 MET Chi-restraints excluded: chain B residue 89 LYS Chi-restraints excluded: chain C residue 78 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 19 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 chunk 13 optimal weight: 0.4980 chunk 3 optimal weight: 0.7980 chunk 23 optimal weight: 0.5980 chunk 21 optimal weight: 0.6980 chunk 0 optimal weight: 0.6980 chunk 4 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3710 r_free = 0.3710 target = 0.157100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.140311 restraints weight = 1732.096| |-----------------------------------------------------------------------------| r_work (start): 0.3547 rms_B_bonded: 1.14 r_work: 0.3423 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3285 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 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 : 0.003 0.029 2115 Z= 0.121 Angle : 0.436 6.409 2832 Z= 0.228 Chirality : 0.034 0.108 333 Planarity : 0.002 0.027 357 Dihedral : 3.242 10.266 285 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 4.63 % Allowed : 25.93 % Favored : 69.44 % 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: 4.27 (0.49), residues: 252 helix: 2.97 (0.31), residues: 237 sheet: None (None), residues: 0 loop : -0.43 (1.07), residues: 15 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 39 TYR 0.008 0.002 TYR C 20 PHE 0.005 0.001 PHE A 88 HIS 0.001 0.000 HIS C 36 Details of bonding type rmsd covalent geometry : bond 0.00260 ( 2109) covalent geometry : angle 0.43552 ( 2832) hydrogen bonds : bond 0.04630 ( 172) hydrogen bonds : angle 3.41107 ( 516) metal coordination : bond 0.00231 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 504 Ramachandran restraints generated. 252 Oldfield, 0 Emsley, 252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 504 Ramachandran restraints generated. 252 Oldfield, 0 Emsley, 252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 53 time to evaluate : 0.082 Fit side-chains REVERT: B 7 GLU cc_start: 0.7099 (mp0) cc_final: 0.6854 (tt0) REVERT: B 39 ARG cc_start: 0.8052 (OUTLIER) cc_final: 0.6829 (ttp-170) REVERT: B 48 GLU cc_start: 0.8070 (mt-10) cc_final: 0.7767 (mt-10) outliers start: 10 outliers final: 6 residues processed: 54 average time/residue: 0.8529 time to fit residues: 46.5737 Evaluate side-chains 59 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 52 time to evaluate : 0.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 39 ARG Chi-restraints excluded: chain B residue 63 MET Chi-restraints excluded: chain B residue 89 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 6 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 10 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- 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 = 0.3658 r_free = 0.3658 target = 0.152305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.135090 restraints weight = 1783.671| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 1.20 r_work: 0.3336 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3192 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.1307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.026 2115 Z= 0.200 Angle : 0.535 6.159 2832 Z= 0.280 Chirality : 0.039 0.124 333 Planarity : 0.003 0.019 357 Dihedral : 3.503 12.120 285 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % Rotamer: Outliers : 4.63 % Allowed : 26.85 % Favored : 68.52 % 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: 3.64 (0.49), residues: 252 helix: 2.61 (0.31), residues: 237 sheet: None (None), residues: 0 loop : -1.44 (1.03), residues: 15 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 39 TYR 0.013 0.002 TYR C 20 PHE 0.009 0.002 PHE A 88 HIS 0.003 0.001 HIS C 36 Details of bonding type rmsd covalent geometry : bond 0.00486 ( 2109) covalent geometry : angle 0.53539 ( 2832) hydrogen bonds : bond 0.06214 ( 172) hydrogen bonds : angle 3.71092 ( 516) metal coordination : bond 0.00314 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 504 Ramachandran restraints generated. 252 Oldfield, 0 Emsley, 252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 504 Ramachandran restraints generated. 252 Oldfield, 0 Emsley, 252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 58 time to evaluate : 0.082 Fit side-chains REVERT: B 7 GLU cc_start: 0.7171 (mp0) cc_final: 0.6950 (tt0) REVERT: B 39 ARG cc_start: 0.8060 (OUTLIER) cc_final: 0.6840 (ttp-170) REVERT: B 48 GLU cc_start: 0.8134 (mt-10) cc_final: 0.7824 (mt-10) REVERT: C 48 GLU cc_start: 0.7249 (mt-10) cc_final: 0.7032 (mt-10) REVERT: C 78 ASP cc_start: 0.8325 (OUTLIER) cc_final: 0.8074 (m-30) outliers start: 10 outliers final: 4 residues processed: 58 average time/residue: 1.0045 time to fit residues: 58.8459 Evaluate side-chains 60 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 54 time to evaluate : 0.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 39 ARG Chi-restraints excluded: chain B residue 63 MET Chi-restraints excluded: chain C residue 78 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 6 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 19 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 7 optimal weight: 0.7980 chunk 18 optimal weight: 2.9990 chunk 4 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 = 0.3680 r_free = 0.3680 target = 0.153989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.137857 restraints weight = 1781.992| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 1.10 r_work: 0.3381 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3242 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.1312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 2115 Z= 0.164 Angle : 0.506 5.488 2832 Z= 0.266 Chirality : 0.037 0.119 333 Planarity : 0.003 0.025 357 Dihedral : 3.420 11.445 285 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 3.70 % Allowed : 28.70 % Favored : 67.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.80 (0.49), residues: 252 helix: 2.72 (0.31), residues: 237 sheet: None (None), residues: 0 loop : -1.59 (1.02), residues: 15 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 39 TYR 0.009 0.002 TYR C 41 PHE 0.007 0.001 PHE A 88 HIS 0.002 0.001 HIS C 36 Details of bonding type rmsd covalent geometry : bond 0.00383 ( 2109) covalent geometry : angle 0.50574 ( 2832) hydrogen bonds : bond 0.05537 ( 172) hydrogen bonds : angle 3.62254 ( 516) metal coordination : bond 0.00268 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 504 Ramachandran restraints generated. 252 Oldfield, 0 Emsley, 252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 504 Ramachandran restraints generated. 252 Oldfield, 0 Emsley, 252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 52 time to evaluate : 0.051 Fit side-chains REVERT: B 39 ARG cc_start: 0.8061 (OUTLIER) cc_final: 0.6872 (ttp-170) REVERT: B 48 GLU cc_start: 0.8122 (mt-10) cc_final: 0.7820 (mt-10) REVERT: C 39 ARG cc_start: 0.8315 (ttm-80) cc_final: 0.7810 (tpp-160) REVERT: C 78 ASP cc_start: 0.8326 (OUTLIER) cc_final: 0.8100 (m-30) outliers start: 8 outliers final: 5 residues processed: 53 average time/residue: 0.8493 time to fit residues: 45.5542 Evaluate side-chains 59 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 52 time to evaluate : 0.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 39 ARG Chi-restraints excluded: chain B residue 63 MET Chi-restraints excluded: chain C residue 78 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 13 optimal weight: 0.0070 chunk 23 optimal weight: 0.9990 chunk 0 optimal weight: 5.9990 chunk 15 optimal weight: 0.9990 chunk 7 optimal weight: 0.5980 chunk 4 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 2 optimal weight: 7.9990 chunk 11 optimal weight: 0.7980 chunk 1 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 overall best weight: 0.6400 ------------------------------------------------------------------------------- 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 = 0.3709 r_free = 0.3709 target = 0.156393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.139879 restraints weight = 1796.900| |-----------------------------------------------------------------------------| r_work (start): 0.3538 rms_B_bonded: 1.14 r_work: 0.3410 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3271 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.1399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 2115 Z= 0.124 Angle : 0.450 5.141 2832 Z= 0.238 Chirality : 0.035 0.119 333 Planarity : 0.003 0.031 357 Dihedral : 3.296 10.435 285 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 3.24 % Allowed : 29.63 % Favored : 67.13 % 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: 4.19 (0.49), residues: 252 helix: 2.96 (0.31), residues: 237 sheet: None (None), residues: 0 loop : -1.25 (1.05), residues: 15 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 39 TYR 0.008 0.002 TYR A 41 PHE 0.006 0.001 PHE A 88 HIS 0.001 0.000 HIS C 47 Details of bonding type rmsd covalent geometry : bond 0.00267 ( 2109) covalent geometry : angle 0.44971 ( 2832) hydrogen bonds : bond 0.04705 ( 172) hydrogen bonds : angle 3.45495 ( 516) metal coordination : bond 0.00234 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 504 Ramachandran restraints generated. 252 Oldfield, 0 Emsley, 252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 504 Ramachandran restraints generated. 252 Oldfield, 0 Emsley, 252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 50 time to evaluate : 0.082 Fit side-chains REVERT: B 6 MET cc_start: 0.6533 (mmp) cc_final: 0.6248 (mmp) REVERT: B 39 ARG cc_start: 0.8036 (OUTLIER) cc_final: 0.6806 (ttp-170) REVERT: C 39 ARG cc_start: 0.8285 (ttm-80) cc_final: 0.7804 (tpp-160) REVERT: C 78 ASP cc_start: 0.8317 (OUTLIER) cc_final: 0.8101 (m-30) outliers start: 7 outliers final: 4 residues processed: 50 average time/residue: 0.7444 time to fit residues: 37.6330 Evaluate side-chains 55 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 49 time to evaluate : 0.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 39 ARG Chi-restraints excluded: chain B residue 63 MET Chi-restraints excluded: chain C residue 78 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 15 optimal weight: 0.9990 chunk 7 optimal weight: 0.4980 chunk 10 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 22 optimal weight: 0.5980 chunk 8 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 12 optimal weight: 0.7980 chunk 4 optimal weight: 0.4980 chunk 3 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.156546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.139830 restraints weight = 1814.857| |-----------------------------------------------------------------------------| r_work (start): 0.3532 rms_B_bonded: 1.16 r_work: 0.3405 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3264 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.1406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 2115 Z= 0.125 Angle : 0.451 5.229 2832 Z= 0.238 Chirality : 0.035 0.119 333 Planarity : 0.002 0.029 357 Dihedral : 3.290 10.350 285 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 3.24 % Allowed : 29.63 % Favored : 67.13 % 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: 4.21 (0.49), residues: 252 helix: 2.96 (0.31), residues: 237 sheet: None (None), residues: 0 loop : -1.07 (1.08), residues: 15 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 39 TYR 0.008 0.002 TYR A 41 PHE 0.006 0.001 PHE A 88 HIS 0.001 0.000 HIS C 36 Details of bonding type rmsd covalent geometry : bond 0.00270 ( 2109) covalent geometry : angle 0.45078 ( 2832) hydrogen bonds : bond 0.04726 ( 172) hydrogen bonds : angle 3.46622 ( 516) metal coordination : bond 0.00229 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 504 Ramachandran restraints generated. 252 Oldfield, 0 Emsley, 252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 504 Ramachandran restraints generated. 252 Oldfield, 0 Emsley, 252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 50 time to evaluate : 0.089 Fit side-chains REVERT: B 6 MET cc_start: 0.6518 (mmp) cc_final: 0.6245 (mmp) REVERT: B 18 GLU cc_start: 0.7187 (mt-10) cc_final: 0.6515 (mm-30) REVERT: B 39 ARG cc_start: 0.8045 (OUTLIER) cc_final: 0.6807 (ttp-170) REVERT: B 48 GLU cc_start: 0.8111 (mt-10) cc_final: 0.7773 (mt-10) REVERT: C 39 ARG cc_start: 0.8301 (ttm-80) cc_final: 0.7818 (tpp-160) REVERT: C 78 ASP cc_start: 0.8326 (OUTLIER) cc_final: 0.8109 (m-30) outliers start: 7 outliers final: 5 residues processed: 51 average time/residue: 0.8546 time to fit residues: 44.0645 Evaluate side-chains 55 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 48 time to evaluate : 0.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 39 ARG Chi-restraints excluded: chain B residue 63 MET Chi-restraints excluded: chain C residue 78 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 16 optimal weight: 0.9980 chunk 14 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 1 optimal weight: 0.9990 chunk 18 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 7 optimal weight: 0.6980 chunk 20 optimal weight: 0.5980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3704 r_free = 0.3704 target = 0.155774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.139040 restraints weight = 1809.727| |-----------------------------------------------------------------------------| r_work (start): 0.3530 rms_B_bonded: 1.16 r_work: 0.3402 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3263 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.1446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 2115 Z= 0.135 Angle : 0.463 5.163 2832 Z= 0.245 Chirality : 0.035 0.121 333 Planarity : 0.003 0.031 357 Dihedral : 3.325 10.532 285 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 3.24 % Allowed : 28.70 % Favored : 68.06 % 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: 4.11 (0.49), residues: 252 helix: 2.90 (0.31), residues: 237 sheet: None (None), residues: 0 loop : -1.10 (1.07), residues: 15 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 39 TYR 0.009 0.002 TYR C 20 PHE 0.006 0.001 PHE A 88 HIS 0.001 0.000 HIS C 36 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 2109) covalent geometry : angle 0.46347 ( 2832) hydrogen bonds : bond 0.04967 ( 172) hydrogen bonds : angle 3.49817 ( 516) metal coordination : bond 0.00242 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1098.49 seconds wall clock time: 19 minutes 18.31 seconds (1158.31 seconds total)