Starting phenix.real_space_refine on Tue Feb 3 12:19:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9xbk_66703/02_2026/9xbk_66703.cif Found real_map, /net/cci-nas-00/data/ceres_data/9xbk_66703/02_2026/9xbk_66703.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9xbk_66703/02_2026/9xbk_66703.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9xbk_66703/02_2026/9xbk_66703.map" model { file = "/net/cci-nas-00/data/ceres_data/9xbk_66703/02_2026/9xbk_66703.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9xbk_66703/02_2026/9xbk_66703.cif" } resolution = 2.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.001 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 3 Type Number sf(0) Gaussians C 1040 2.51 5 N 370 2.21 5 O 375 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model 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: 1785 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 357 Classifications: {'peptide': 43} Link IDs: {'TRANS': 42} Chain breaks: 1 Restraints were copied for chains: B, C, D, E Time building chain proxies: 0.24, per 1000 atoms: 0.13 Number of scatterers: 1785 At special positions: 0 Unit cell: (53.95, 63.08, 43.99, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 375 8.00 N 370 7.00 C 1040 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: 0.08 Conformation dependent library (CDL) restraints added in 36.7 milliseconds 390 Ramachandran restraints generated. 195 Oldfield, 0 Emsley, 195 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 380 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 4 sheets defined 0.0% alpha, 39.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.04 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'D' and resid 18 through 19 removed outlier: 6.770A pdb=" N GLN B 18 " --> pdb=" O ASN D 19 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N GLN A 18 " --> pdb=" O ASN B 19 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 22 through 25 removed outlier: 6.434A pdb=" N GLN B 23 " --> pdb=" O GLN D 24 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N GLN A 23 " --> pdb=" O GLN B 24 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 28 through 37 removed outlier: 6.530A pdb=" N ARG A 28 " --> pdb=" O TYR C 29 " (cutoff:3.500A) removed outlier: 8.126A pdb=" N GLY C 31 " --> pdb=" O ARG A 28 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N GLN A 30 " --> pdb=" O GLY C 31 " (cutoff:3.500A) removed outlier: 8.384A pdb=" N GLN C 33 " --> pdb=" O GLN A 30 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N TYR A 32 " --> pdb=" O GLN C 33 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N TYR C 35 " --> pdb=" O TYR A 32 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ALA A 34 " --> pdb=" O TYR C 35 " (cutoff:3.500A) removed outlier: 7.952A pdb=" N ALA C 37 " --> pdb=" O ALA A 34 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N ASN A 36 " --> pdb=" O ALA C 37 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ARG C 28 " --> pdb=" O TYR E 29 " (cutoff:3.500A) removed outlier: 8.131A pdb=" N GLY E 31 " --> pdb=" O ARG C 28 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N GLN C 30 " --> pdb=" O GLY E 31 " (cutoff:3.500A) removed outlier: 8.390A pdb=" N GLN E 33 " --> pdb=" O GLN C 30 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N TYR C 32 " --> pdb=" O GLN E 33 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N TYR E 35 " --> pdb=" O TYR C 32 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ALA C 34 " --> pdb=" O TYR E 35 " (cutoff:3.500A) removed outlier: 7.958A pdb=" N ALA E 37 " --> pdb=" O ALA C 34 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N ASN C 36 " --> pdb=" O ALA E 37 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 109 through 113 removed outlier: 6.249A pdb=" N LEU B 110 " --> pdb=" O GLN D 111 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N TYR D 113 " --> pdb=" O LEU B 110 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N GLY B 112 " --> pdb=" O TYR D 113 " (cutoff:3.500A) 38 hydrogen bonds defined for protein. 114 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: 0.14 Time building geometry restraints manager: 0.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.29: 340 1.29 - 1.35: 360 1.35 - 1.42: 210 1.42 - 1.48: 210 1.48 - 1.54: 685 Bond restraints: 1805 Sorted by residual: bond pdb=" N ASN A 9 " pdb=" CA ASN A 9 " ideal model delta sigma weight residual 1.460 1.505 -0.046 1.28e-02 6.10e+03 1.28e+01 bond pdb=" N ASN E 9 " pdb=" CA ASN E 9 " ideal model delta sigma weight residual 1.460 1.505 -0.045 1.28e-02 6.10e+03 1.25e+01 bond pdb=" N ASN C 9 " pdb=" CA ASN C 9 " ideal model delta sigma weight residual 1.460 1.505 -0.045 1.28e-02 6.10e+03 1.24e+01 bond pdb=" N ASN B 9 " pdb=" CA ASN B 9 " ideal model delta sigma weight residual 1.460 1.505 -0.045 1.28e-02 6.10e+03 1.23e+01 bond pdb=" N ASN D 9 " pdb=" CA ASN D 9 " ideal model delta sigma weight residual 1.460 1.504 -0.045 1.28e-02 6.10e+03 1.23e+01 ... (remaining 1800 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.24: 2137 1.24 - 2.49: 218 2.49 - 3.73: 40 3.73 - 4.97: 15 4.97 - 6.21: 10 Bond angle restraints: 2420 Sorted by residual: angle pdb=" N ASN D 21 " pdb=" CA ASN D 21 " pdb=" C ASN D 21 " ideal model delta sigma weight residual 110.24 115.70 -5.46 1.47e+00 4.63e-01 1.38e+01 angle pdb=" N ASN C 21 " pdb=" CA ASN C 21 " pdb=" C ASN C 21 " ideal model delta sigma weight residual 110.24 115.66 -5.42 1.47e+00 4.63e-01 1.36e+01 angle pdb=" N ASN A 21 " pdb=" CA ASN A 21 " pdb=" C ASN A 21 " ideal model delta sigma weight residual 110.24 115.65 -5.41 1.47e+00 4.63e-01 1.35e+01 angle pdb=" N ASN B 21 " pdb=" CA ASN B 21 " pdb=" C ASN B 21 " ideal model delta sigma weight residual 110.24 115.65 -5.41 1.47e+00 4.63e-01 1.35e+01 angle pdb=" N ASN E 21 " pdb=" CA ASN E 21 " pdb=" C ASN E 21 " ideal model delta sigma weight residual 110.24 115.64 -5.40 1.47e+00 4.63e-01 1.35e+01 ... (remaining 2415 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.59: 925 17.59 - 35.18: 70 35.18 - 52.77: 50 52.77 - 70.35: 10 70.35 - 87.94: 5 Dihedral angle restraints: 1060 sinusoidal: 445 harmonic: 615 Sorted by residual: dihedral pdb=" CA TYR E 29 " pdb=" C TYR E 29 " pdb=" N GLN E 30 " pdb=" CA GLN E 30 " ideal model delta harmonic sigma weight residual 180.00 164.91 15.09 0 5.00e+00 4.00e-02 9.11e+00 dihedral pdb=" CA TYR C 29 " pdb=" C TYR C 29 " pdb=" N GLN C 30 " pdb=" CA GLN C 30 " ideal model delta harmonic sigma weight residual 180.00 164.92 15.08 0 5.00e+00 4.00e-02 9.10e+00 dihedral pdb=" CA TYR A 29 " pdb=" C TYR A 29 " pdb=" N GLN A 30 " pdb=" CA GLN A 30 " ideal model delta harmonic sigma weight residual 180.00 164.92 15.08 0 5.00e+00 4.00e-02 9.09e+00 ... (remaining 1057 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 139 0.036 - 0.073: 36 0.073 - 0.109: 10 0.109 - 0.145: 3 0.145 - 0.181: 7 Chirality restraints: 195 Sorted by residual: chirality pdb=" CA ASN A 9 " pdb=" N ASN A 9 " pdb=" C ASN A 9 " pdb=" CB ASN A 9 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.22e-01 chirality pdb=" CA ASN B 9 " pdb=" N ASN B 9 " pdb=" C ASN B 9 " pdb=" CB ASN B 9 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.03e-01 chirality pdb=" CA ASN D 9 " pdb=" N ASN D 9 " pdb=" C ASN D 9 " pdb=" CB ASN D 9 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.02e-01 ... (remaining 192 not shown) Planarity restraints: 370 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR D 29 " 0.008 2.00e-02 2.50e+03 1.61e-02 2.58e+00 pdb=" C TYR D 29 " -0.028 2.00e-02 2.50e+03 pdb=" O TYR D 29 " 0.010 2.00e-02 2.50e+03 pdb=" N GLN D 30 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR B 29 " 0.008 2.00e-02 2.50e+03 1.60e-02 2.56e+00 pdb=" C TYR B 29 " -0.028 2.00e-02 2.50e+03 pdb=" O TYR B 29 " 0.010 2.00e-02 2.50e+03 pdb=" N GLN B 30 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR E 29 " 0.008 2.00e-02 2.50e+03 1.58e-02 2.51e+00 pdb=" C TYR E 29 " -0.027 2.00e-02 2.50e+03 pdb=" O TYR E 29 " 0.010 2.00e-02 2.50e+03 pdb=" N GLN E 30 " 0.009 2.00e-02 2.50e+03 ... (remaining 367 not shown) Histogram of nonbonded interaction distances: 2.63 - 3.09: 1262 3.09 - 3.54: 1719 3.54 - 3.99: 3082 3.99 - 4.45: 3493 4.45 - 4.90: 5836 Nonbonded interactions: 15392 Sorted by model distance: nonbonded pdb=" O ASN C 19 " pdb=" N GLY E 20 " model vdw 2.633 3.120 nonbonded pdb=" N GLY B 20 " pdb=" O ASN D 19 " model vdw 2.633 3.120 nonbonded pdb=" N GLY A 20 " pdb=" O ASN B 19 " model vdw 2.633 3.120 nonbonded pdb=" O ASN A 19 " pdb=" N GLY C 20 " model vdw 2.634 3.120 nonbonded pdb=" O GLN B 114 " pdb=" CB GLN B 114 " model vdw 2.683 2.752 ... (remaining 15387 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' selection = chain 'D' selection = chain 'E' } 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: 0.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.030 Check model and map are aligned: 0.000 Set scattering table: 0.020 Process input model: 2.800 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:6.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8695 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.046 1805 Z= 0.423 Angle : 0.914 6.212 2420 Z= 0.569 Chirality : 0.050 0.181 195 Planarity : 0.007 0.043 370 Dihedral : 19.095 87.943 680 Min Nonbonded Distance : 2.633 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 0.00 % Allowed : 20.00 % Favored : 80.00 % 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: -5.00 (0.29), residues: 195 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.81 (0.22), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 28 TYR 0.020 0.002 TYR B 32 Details of bonding type rmsd covalent geometry : bond 0.00678 ( 1805) covalent geometry : angle 0.91400 ( 2420) hydrogen bonds : bond 0.10556 ( 38) hydrogen bonds : angle 11.12372 ( 114) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 390 Ramachandran restraints generated. 195 Oldfield, 0 Emsley, 195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 390 Ramachandran restraints generated. 195 Oldfield, 0 Emsley, 195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.072 Fit side-chains REVERT: B 6 GLN cc_start: 0.8164 (mt0) cc_final: 0.7791 (mt0) REVERT: B 11 GLN cc_start: 0.8535 (mm110) cc_final: 0.8332 (mm-40) REVERT: C 11 GLN cc_start: 0.8615 (mm110) cc_final: 0.8397 (mm110) REVERT: D 11 GLN cc_start: 0.8705 (mm110) cc_final: 0.8462 (mm-40) outliers start: 0 outliers final: 0 residues processed: 41 average time/residue: 1.0584 time to fit residues: 43.7942 Evaluate side-chains 38 residues out of total 175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 38 time to evaluate : 0.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 12 optimal weight: 10.0000 chunk 13 optimal weight: 3.9990 chunk 1 optimal weight: 9.9990 chunk 8 optimal weight: 3.9990 chunk 16 optimal weight: 0.6980 chunk 15 optimal weight: 8.9990 chunk 9 optimal weight: 3.9990 chunk 11 optimal weight: 8.9990 chunk 18 optimal weight: 7.9990 chunk 6 optimal weight: 0.9990 chunk 4 optimal weight: 3.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 GLN A 108 ASN A 109 ASN B 11 GLN B 22 GLN B 24 GLN B 108 ASN B 109 ASN C 11 GLN C 108 ASN C 109 ASN C 114 GLN D 11 GLN D 12 ASN D 30 GLN D 108 ASN D 109 ASN E 108 ASN E 109 ASN E 114 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.111636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.085687 restraints weight = 1913.207| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 2.04 r_work: 0.3130 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2991 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8732 moved from start: 0.1962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.015 1805 Z= 0.160 Angle : 0.648 6.041 2420 Z= 0.366 Chirality : 0.042 0.126 195 Planarity : 0.003 0.020 370 Dihedral : 5.004 15.004 245 Min Nonbonded Distance : 2.638 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.14 % Allowed : 12.00 % Favored : 86.86 % 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 (0.34), residues: 195 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.20 (0.26), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 28 TYR 0.019 0.002 TYR D 32 Details of bonding type rmsd covalent geometry : bond 0.00345 ( 1805) covalent geometry : angle 0.64810 ( 2420) hydrogen bonds : bond 0.03481 ( 38) hydrogen bonds : angle 6.58070 ( 114) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 390 Ramachandran restraints generated. 195 Oldfield, 0 Emsley, 195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 390 Ramachandran restraints generated. 195 Oldfield, 0 Emsley, 195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 47 time to evaluate : 0.072 Fit side-chains REVERT: B 6 GLN cc_start: 0.8336 (mt0) cc_final: 0.8024 (mt0) REVERT: B 28 ARG cc_start: 0.8089 (mtt90) cc_final: 0.7510 (mpt90) REVERT: D 6 GLN cc_start: 0.8641 (mt0) cc_final: 0.8300 (mt0) outliers start: 2 outliers final: 0 residues processed: 48 average time/residue: 1.0016 time to fit residues: 48.5288 Evaluate side-chains 46 residues out of total 175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 3 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 11 optimal weight: 1.9990 chunk 5 optimal weight: 9.9990 chunk 12 optimal weight: 10.0000 chunk 19 optimal weight: 0.7980 chunk 10 optimal weight: 8.9990 chunk 14 optimal weight: 7.9990 chunk 17 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 9 ASN B 24 GLN C 11 GLN C 19 ASN C 22 GLN C 114 GLN D 19 ASN D 22 GLN E 114 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.111678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.085411 restraints weight = 1923.824| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 2.06 r_work: 0.3149 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3008 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8734 moved from start: 0.2367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.012 1805 Z= 0.133 Angle : 0.589 5.770 2420 Z= 0.335 Chirality : 0.041 0.109 195 Planarity : 0.002 0.023 370 Dihedral : 4.540 13.180 245 Min Nonbonded Distance : 2.644 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 1.14 % Allowed : 12.00 % Favored : 86.86 % 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: -4.22 (0.37), residues: 195 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.21 (0.28), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 28 TYR 0.018 0.002 TYR D 32 Details of bonding type rmsd covalent geometry : bond 0.00280 ( 1805) covalent geometry : angle 0.58922 ( 2420) hydrogen bonds : bond 0.03080 ( 38) hydrogen bonds : angle 6.15824 ( 114) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 390 Ramachandran restraints generated. 195 Oldfield, 0 Emsley, 195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 390 Ramachandran restraints generated. 195 Oldfield, 0 Emsley, 195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 50 time to evaluate : 0.071 Fit side-chains REVERT: A 6 GLN cc_start: 0.8511 (mt0) cc_final: 0.8262 (mt0) REVERT: B 6 GLN cc_start: 0.8363 (mt0) cc_final: 0.7997 (mt0) REVERT: B 28 ARG cc_start: 0.8080 (mtt90) cc_final: 0.7485 (mpt90) outliers start: 2 outliers final: 0 residues processed: 51 average time/residue: 0.9224 time to fit residues: 47.5244 Evaluate side-chains 49 residues out of total 175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 0.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 6 optimal weight: 7.9990 chunk 0 optimal weight: 20.0000 chunk 4 optimal weight: 3.9990 chunk 7 optimal weight: 9.9990 chunk 14 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 2 optimal weight: 0.9980 chunk 19 optimal weight: 0.0050 chunk 8 optimal weight: 6.9990 chunk 9 optimal weight: 6.9990 chunk 12 optimal weight: 0.4980 overall best weight: 1.6998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 24 GLN C 114 GLN E 114 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.112682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.086770 restraints weight = 1929.344| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 2.04 r_work: 0.3163 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3020 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8735 moved from start: 0.2555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.010 1805 Z= 0.112 Angle : 0.569 6.503 2420 Z= 0.320 Chirality : 0.041 0.131 195 Planarity : 0.002 0.024 370 Dihedral : 4.243 12.260 245 Min Nonbonded Distance : 2.650 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Rotamer: Outliers : 0.57 % Allowed : 14.29 % Favored : 85.14 % 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: -4.20 (0.39), residues: 195 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.19 (0.30), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 28 TYR 0.017 0.002 TYR D 32 Details of bonding type rmsd covalent geometry : bond 0.00233 ( 1805) covalent geometry : angle 0.56934 ( 2420) hydrogen bonds : bond 0.02803 ( 38) hydrogen bonds : angle 5.99164 ( 114) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 390 Ramachandran restraints generated. 195 Oldfield, 0 Emsley, 195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 390 Ramachandran restraints generated. 195 Oldfield, 0 Emsley, 195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 48 time to evaluate : 0.074 Fit side-chains REVERT: A 6 GLN cc_start: 0.8506 (mt0) cc_final: 0.8267 (mt0) REVERT: A 114 GLN cc_start: 0.7843 (mt0) cc_final: 0.7632 (mt0) REVERT: B 6 GLN cc_start: 0.8371 (mt0) cc_final: 0.8102 (mt0) REVERT: B 28 ARG cc_start: 0.8092 (mtt90) cc_final: 0.7516 (mpt90) outliers start: 1 outliers final: 0 residues processed: 48 average time/residue: 0.9721 time to fit residues: 47.0971 Evaluate side-chains 46 residues out of total 175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 0 optimal weight: 20.0000 chunk 18 optimal weight: 7.9990 chunk 1 optimal weight: 10.0000 chunk 12 optimal weight: 9.9990 chunk 13 optimal weight: 4.9990 chunk 16 optimal weight: 5.9990 chunk 11 optimal weight: 9.9990 chunk 7 optimal weight: 9.9990 chunk 5 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 24 GLN C 114 GLN E 9 ASN E 114 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.109925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.084153 restraints weight = 1947.972| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 2.05 r_work: 0.3125 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8753 moved from start: 0.2585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.019 1805 Z= 0.194 Angle : 0.610 6.524 2420 Z= 0.348 Chirality : 0.042 0.142 195 Planarity : 0.003 0.024 370 Dihedral : 4.498 13.235 245 Min Nonbonded Distance : 2.638 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 1.71 % Allowed : 13.71 % Favored : 84.57 % 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: -4.17 (0.40), residues: 195 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.17 (0.30), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 28 TYR 0.022 0.002 TYR D 32 Details of bonding type rmsd covalent geometry : bond 0.00415 ( 1805) covalent geometry : angle 0.61042 ( 2420) hydrogen bonds : bond 0.03492 ( 38) hydrogen bonds : angle 5.98893 ( 114) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 390 Ramachandran restraints generated. 195 Oldfield, 0 Emsley, 195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 390 Ramachandran restraints generated. 195 Oldfield, 0 Emsley, 195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 46 time to evaluate : 0.069 Fit side-chains REVERT: A 114 GLN cc_start: 0.7863 (mt0) cc_final: 0.7645 (mt0) REVERT: B 6 GLN cc_start: 0.8489 (mt0) cc_final: 0.8236 (mt0) REVERT: B 28 ARG cc_start: 0.8085 (mtt90) cc_final: 0.7501 (mpt90) REVERT: C 17 ARG cc_start: 0.8837 (OUTLIER) cc_final: 0.8514 (ttt180) outliers start: 3 outliers final: 0 residues processed: 47 average time/residue: 0.8333 time to fit residues: 39.5993 Evaluate side-chains 47 residues out of total 175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 46 time to evaluate : 0.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 17 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 0 optimal weight: 10.0000 chunk 17 optimal weight: 5.9990 chunk 1 optimal weight: 9.9990 chunk 18 optimal weight: 8.9990 chunk 6 optimal weight: 2.9990 chunk 5 optimal weight: 5.9990 chunk 19 optimal weight: 0.4980 chunk 14 optimal weight: 0.8980 chunk 16 optimal weight: 3.9990 chunk 15 optimal weight: 8.9990 chunk 12 optimal weight: 0.5980 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 24 GLN C 114 GLN E 9 ASN E 114 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.111698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.085303 restraints weight = 1914.703| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 2.07 r_work: 0.3147 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3003 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8736 moved from start: 0.2710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.010 1805 Z= 0.117 Angle : 0.554 5.546 2420 Z= 0.315 Chirality : 0.040 0.111 195 Planarity : 0.002 0.024 370 Dihedral : 4.166 14.959 245 Min Nonbonded Distance : 2.652 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.71 % Allowed : 13.71 % Favored : 84.57 % 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: -4.15 (0.40), residues: 195 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.16 (0.31), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 28 TYR 0.017 0.002 TYR D 32 Details of bonding type rmsd covalent geometry : bond 0.00241 ( 1805) covalent geometry : angle 0.55428 ( 2420) hydrogen bonds : bond 0.02866 ( 38) hydrogen bonds : angle 5.93933 ( 114) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 390 Ramachandran restraints generated. 195 Oldfield, 0 Emsley, 195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 390 Ramachandran restraints generated. 195 Oldfield, 0 Emsley, 195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 47 time to evaluate : 0.077 Fit side-chains REVERT: B 28 ARG cc_start: 0.8074 (mtt90) cc_final: 0.7468 (mpt90) REVERT: C 17 ARG cc_start: 0.8841 (OUTLIER) cc_final: 0.8506 (ttt180) outliers start: 3 outliers final: 1 residues processed: 48 average time/residue: 0.6230 time to fit residues: 30.2446 Evaluate side-chains 49 residues out of total 175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 47 time to evaluate : 0.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 17 ARG Chi-restraints excluded: chain D residue 110 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 15 optimal weight: 0.3980 chunk 2 optimal weight: 5.9990 chunk 1 optimal weight: 10.0000 chunk 14 optimal weight: 5.9990 chunk 13 optimal weight: 7.9990 chunk 7 optimal weight: 4.9990 chunk 8 optimal weight: 2.9990 chunk 4 optimal weight: 10.0000 chunk 18 optimal weight: 6.9990 chunk 11 optimal weight: 9.9990 chunk 17 optimal weight: 4.9990 overall best weight: 3.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 GLN B 24 GLN C 114 GLN E 9 ASN E 22 GLN E 114 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.109682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.083704 restraints weight = 1917.934| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 2.03 r_work: 0.3124 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8759 moved from start: 0.2710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.021 1805 Z= 0.220 Angle : 0.621 6.914 2420 Z= 0.353 Chirality : 0.042 0.162 195 Planarity : 0.003 0.025 370 Dihedral : 4.528 15.966 245 Min Nonbonded Distance : 2.642 Molprobity Statistics. All-atom Clashscore : 2.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 0.57 % Allowed : 14.86 % Favored : 84.57 % 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: -4.10 (0.40), residues: 195 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.12 (0.31), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 28 TYR 0.023 0.002 TYR D 32 Details of bonding type rmsd covalent geometry : bond 0.00472 ( 1805) covalent geometry : angle 0.62076 ( 2420) hydrogen bonds : bond 0.03700 ( 38) hydrogen bonds : angle 5.88788 ( 114) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 390 Ramachandran restraints generated. 195 Oldfield, 0 Emsley, 195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 390 Ramachandran restraints generated. 195 Oldfield, 0 Emsley, 195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 43 time to evaluate : 0.042 Fit side-chains REVERT: B 28 ARG cc_start: 0.8088 (mtt90) cc_final: 0.7481 (mpt90) REVERT: C 17 ARG cc_start: 0.8837 (OUTLIER) cc_final: 0.8514 (ttt180) REVERT: C 114 GLN cc_start: 0.7912 (mt0) cc_final: 0.7629 (mp10) outliers start: 1 outliers final: 0 residues processed: 43 average time/residue: 0.6011 time to fit residues: 26.1243 Evaluate side-chains 44 residues out of total 175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 43 time to evaluate : 0.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 17 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 9 optimal weight: 8.9990 chunk 19 optimal weight: 0.0040 chunk 8 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 6 optimal weight: 3.9990 chunk 7 optimal weight: 9.9990 chunk 14 optimal weight: 0.8980 chunk 2 optimal weight: 0.9990 chunk 12 optimal weight: 0.0970 chunk 10 optimal weight: 0.9980 chunk 15 optimal weight: 7.9990 overall best weight: 0.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 108 ASN E 9 ASN E 114 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.115234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.088524 restraints weight = 1912.476| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 2.08 r_work: 0.3210 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3071 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8709 moved from start: 0.2977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.011 1805 Z= 0.074 Angle : 0.528 7.002 2420 Z= 0.289 Chirality : 0.039 0.118 195 Planarity : 0.002 0.024 370 Dihedral : 3.742 16.676 245 Min Nonbonded Distance : 2.656 Molprobity Statistics. All-atom Clashscore : 2.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.57 % Allowed : 14.29 % Favored : 85.14 % 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: -4.09 (0.42), residues: 195 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.11 (0.32), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 28 TYR 0.015 0.001 TYR B 32 Details of bonding type rmsd covalent geometry : bond 0.00146 ( 1805) covalent geometry : angle 0.52768 ( 2420) hydrogen bonds : bond 0.02213 ( 38) hydrogen bonds : angle 5.85859 ( 114) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 390 Ramachandran restraints generated. 195 Oldfield, 0 Emsley, 195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 390 Ramachandran restraints generated. 195 Oldfield, 0 Emsley, 195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 48 time to evaluate : 0.070 Fit side-chains REVERT: A 6 GLN cc_start: 0.8556 (mt0) cc_final: 0.8235 (mt0) REVERT: B 17 ARG cc_start: 0.8958 (ttt180) cc_final: 0.8741 (ttt90) REVERT: B 28 ARG cc_start: 0.8090 (mtt90) cc_final: 0.7492 (mpt90) REVERT: D 108 ASN cc_start: 0.7343 (t0) cc_final: 0.7134 (t0) outliers start: 1 outliers final: 0 residues processed: 48 average time/residue: 0.5811 time to fit residues: 28.2392 Evaluate side-chains 46 residues out of total 175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 19 optimal weight: 0.0980 chunk 6 optimal weight: 8.9990 chunk 8 optimal weight: 6.9990 chunk 13 optimal weight: 6.9990 chunk 17 optimal weight: 8.9990 chunk 7 optimal weight: 9.9990 chunk 18 optimal weight: 4.9990 chunk 15 optimal weight: 9.9990 chunk 4 optimal weight: 10.0000 chunk 0 optimal weight: 3.9990 chunk 10 optimal weight: 6.9990 overall best weight: 4.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 114 GLN D 12 ASN D 109 ASN E 9 ASN E 114 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.110089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.083898 restraints weight = 1907.680| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 2.03 r_work: 0.3121 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2978 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8769 moved from start: 0.2783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.026 1805 Z= 0.257 Angle : 0.632 6.871 2420 Z= 0.361 Chirality : 0.042 0.160 195 Planarity : 0.003 0.028 370 Dihedral : 4.566 17.242 245 Min Nonbonded Distance : 2.640 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 0.00 % Allowed : 16.57 % Favored : 83.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.07 (0.41), residues: 195 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.09 (0.31), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 28 TYR 0.025 0.003 TYR D 32 Details of bonding type rmsd covalent geometry : bond 0.00551 ( 1805) covalent geometry : angle 0.63169 ( 2420) hydrogen bonds : bond 0.03929 ( 38) hydrogen bonds : angle 5.89092 ( 114) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 390 Ramachandran restraints generated. 195 Oldfield, 0 Emsley, 195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 390 Ramachandran restraints generated. 195 Oldfield, 0 Emsley, 195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.051 Fit side-chains REVERT: B 28 ARG cc_start: 0.8116 (mtt90) cc_final: 0.7483 (mpt90) outliers start: 0 outliers final: 0 residues processed: 47 average time/residue: 0.5752 time to fit residues: 27.3311 Evaluate side-chains 46 residues out of total 175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 15 optimal weight: 10.0000 chunk 1 optimal weight: 7.9990 chunk 14 optimal weight: 5.9990 chunk 2 optimal weight: 2.9990 chunk 0 optimal weight: 9.9990 chunk 16 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 5 optimal weight: 0.7980 chunk 10 optimal weight: 0.9980 chunk 4 optimal weight: 10.0000 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 19 ASN C 114 GLN D 22 GLN D 108 ASN D 114 GLN E 9 ASN E 114 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.111799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.084880 restraints weight = 1900.852| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 2.07 r_work: 0.3143 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3002 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8755 moved from start: 0.2796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.014 1805 Z= 0.146 Angle : 0.580 6.766 2420 Z= 0.326 Chirality : 0.040 0.137 195 Planarity : 0.002 0.027 370 Dihedral : 4.322 17.930 245 Min Nonbonded Distance : 2.641 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 14.86 % Favored : 85.14 % 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: -4.01 (0.42), residues: 195 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.05 (0.32), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 28 TYR 0.019 0.002 TYR D 32 Details of bonding type rmsd covalent geometry : bond 0.00306 ( 1805) covalent geometry : angle 0.57999 ( 2420) hydrogen bonds : bond 0.03040 ( 38) hydrogen bonds : angle 5.85562 ( 114) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 390 Ramachandran restraints generated. 195 Oldfield, 0 Emsley, 195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 390 Ramachandran restraints generated. 195 Oldfield, 0 Emsley, 195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 0.043 Fit side-chains REVERT: B 28 ARG cc_start: 0.8097 (mtt90) cc_final: 0.7463 (mpt90) REVERT: C 114 GLN cc_start: 0.7944 (mt0) cc_final: 0.7655 (mp10) outliers start: 0 outliers final: 0 residues processed: 49 average time/residue: 0.6212 time to fit residues: 30.7405 Evaluate side-chains 48 residues out of total 175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 0.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 2 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 chunk 9 optimal weight: 6.9990 chunk 4 optimal weight: 9.9990 chunk 11 optimal weight: 10.0000 chunk 7 optimal weight: 6.9990 chunk 15 optimal weight: 5.9990 chunk 8 optimal weight: 0.8980 chunk 10 optimal weight: 0.7980 chunk 1 optimal weight: 7.9990 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 22 GLN D 108 ASN D 114 GLN E 9 ASN E 114 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.113144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.086613 restraints weight = 1904.859| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 2.05 r_work: 0.3173 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3031 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8738 moved from start: 0.2907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.011 1805 Z= 0.096 Angle : 0.546 6.790 2420 Z= 0.304 Chirality : 0.039 0.125 195 Planarity : 0.002 0.028 370 Dihedral : 3.985 18.135 245 Min Nonbonded Distance : 2.640 Molprobity Statistics. All-atom Clashscore : 2.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 0.00 % Allowed : 14.86 % Favored : 85.14 % 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: -3.92 (0.44), residues: 195 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.98 (0.33), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 28 TYR 0.016 0.002 TYR B 32 Details of bonding type rmsd covalent geometry : bond 0.00194 ( 1805) covalent geometry : angle 0.54648 ( 2420) hydrogen bonds : bond 0.02495 ( 38) hydrogen bonds : angle 5.77968 ( 114) =============================================================================== Job complete usr+sys time: 1038.82 seconds wall clock time: 18 minutes 53.47 seconds (1133.47 seconds total)