Starting phenix.real_space_refine on Tue Feb 3 12:24:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9k8t_62180/02_2026/9k8t_62180.cif Found real_map, /net/cci-nas-00/data/ceres_data/9k8t_62180/02_2026/9k8t_62180.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9k8t_62180/02_2026/9k8t_62180.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9k8t_62180/02_2026/9k8t_62180.map" model { file = "/net/cci-nas-00/data/ceres_data/9k8t_62180/02_2026/9k8t_62180.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9k8t_62180/02_2026/9k8t_62180.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 24 5.16 5 C 1224 2.51 5 N 312 2.21 5 O 384 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: 1944 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 179 Classifications: {'peptide': 25} Link IDs: {'TRANS': 24} Chain: "B" Number of atoms: 145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 145 Classifications: {'peptide': 20} Link IDs: {'TRANS': 19} Restraints were copied for chains: C, E, G, I, K, D, F, H, J, L Time building chain proxies: 0.35, per 1000 atoms: 0.18 Number of scatterers: 1944 At special positions: 0 Unit cell: (59.28, 111.28, 31.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 24 16.00 O 384 8.00 N 312 7.00 C 1224 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: 0.16 Conformation dependent library (CDL) restraints added in 83.3 milliseconds 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 540 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 4 sheets defined 0.0% alpha, 13.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.06 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'C' and resid 49 through 54 removed outlier: 6.171A pdb=" N GLU A 49 " --> pdb=" O SER E 50 " (cutoff:3.500A) removed outlier: 8.180A pdb=" N LEU E 52 " --> pdb=" O GLU A 49 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N MET A 51 " --> pdb=" O LEU E 52 " (cutoff:3.500A) removed outlier: 8.540A pdb=" N ILE E 54 " --> pdb=" O MET A 51 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N ASP A 53 " --> pdb=" O ILE E 54 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 67 through 68 removed outlier: 6.457A pdb=" N VAL A 67 " --> pdb=" O VAL E 68 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'I' and resid 49 through 54 removed outlier: 6.171A pdb=" N GLU G 49 " --> pdb=" O SER K 50 " (cutoff:3.500A) removed outlier: 8.181A pdb=" N LEU K 52 " --> pdb=" O GLU G 49 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N MET G 51 " --> pdb=" O LEU K 52 " (cutoff:3.500A) removed outlier: 8.540A pdb=" N ILE K 54 " --> pdb=" O MET G 51 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N ASP G 53 " --> pdb=" O ILE K 54 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'I' and resid 67 through 68 removed outlier: 6.457A pdb=" N VAL G 67 " --> pdb=" O VAL K 68 " (cutoff:3.500A) 12 hydrogen bonds defined for protein. 36 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.24 Time building geometry restraints manager: 0.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 636 1.34 - 1.46: 159 1.46 - 1.57: 1089 1.57 - 1.69: 0 1.69 - 1.80: 48 Bond restraints: 1932 Sorted by residual: bond pdb=" C LEU C 52 " pdb=" O LEU C 52 " ideal model delta sigma weight residual 1.235 1.225 0.011 1.26e-02 6.30e+03 7.22e-01 bond pdb=" C LEU A 52 " pdb=" O LEU A 52 " ideal model delta sigma weight residual 1.235 1.225 0.010 1.26e-02 6.30e+03 6.84e-01 bond pdb=" C LEU G 52 " pdb=" O LEU G 52 " ideal model delta sigma weight residual 1.235 1.225 0.010 1.26e-02 6.30e+03 6.63e-01 bond pdb=" C LEU I 52 " pdb=" O LEU I 52 " ideal model delta sigma weight residual 1.235 1.225 0.010 1.26e-02 6.30e+03 6.23e-01 bond pdb=" C LEU E 52 " pdb=" O LEU E 52 " ideal model delta sigma weight residual 1.235 1.226 0.010 1.26e-02 6.30e+03 5.94e-01 ... (remaining 1927 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.16: 2287 1.16 - 2.32: 225 2.32 - 3.47: 38 3.47 - 4.63: 24 4.63 - 5.79: 12 Bond angle restraints: 2586 Sorted by residual: angle pdb=" C LEU C 52 " pdb=" N ASP C 53 " pdb=" CA ASP C 53 " ideal model delta sigma weight residual 122.36 118.14 4.22 1.60e+00 3.91e-01 6.94e+00 angle pdb=" C LEU G 52 " pdb=" N ASP G 53 " pdb=" CA ASP G 53 " ideal model delta sigma weight residual 122.36 118.17 4.19 1.60e+00 3.91e-01 6.85e+00 angle pdb=" C LEU I 52 " pdb=" N ASP I 53 " pdb=" CA ASP I 53 " ideal model delta sigma weight residual 122.36 118.19 4.17 1.60e+00 3.91e-01 6.79e+00 angle pdb=" C LEU K 52 " pdb=" N ASP K 53 " pdb=" CA ASP K 53 " ideal model delta sigma weight residual 122.36 118.21 4.15 1.60e+00 3.91e-01 6.73e+00 angle pdb=" C LEU A 52 " pdb=" N ASP A 53 " pdb=" CA ASP A 53 " ideal model delta sigma weight residual 122.36 118.21 4.15 1.60e+00 3.91e-01 6.72e+00 ... (remaining 2581 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 9.74: 960 9.74 - 19.46: 132 19.46 - 29.19: 102 29.19 - 38.92: 48 38.92 - 48.65: 12 Dihedral angle restraints: 1254 sinusoidal: 456 harmonic: 798 Sorted by residual: dihedral pdb=" CA LEU L 57 " pdb=" C LEU L 57 " pdb=" N MET L 58 " pdb=" CA MET L 58 " ideal model delta harmonic sigma weight residual 180.00 163.54 16.46 0 5.00e+00 4.00e-02 1.08e+01 dihedral pdb=" CA LEU B 57 " pdb=" C LEU B 57 " pdb=" N MET B 58 " pdb=" CA MET B 58 " ideal model delta harmonic sigma weight residual 180.00 163.56 16.44 0 5.00e+00 4.00e-02 1.08e+01 dihedral pdb=" CA LEU F 57 " pdb=" C LEU F 57 " pdb=" N MET F 58 " pdb=" CA MET F 58 " ideal model delta harmonic sigma weight residual 180.00 163.56 16.44 0 5.00e+00 4.00e-02 1.08e+01 ... (remaining 1251 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 232 0.030 - 0.059: 74 0.059 - 0.089: 14 0.089 - 0.119: 26 0.119 - 0.148: 8 Chirality restraints: 354 Sorted by residual: chirality pdb=" CB ILE B 54 " pdb=" CA ILE B 54 " pdb=" CG1 ILE B 54 " pdb=" CG2 ILE B 54 " both_signs ideal model delta sigma weight residual False 2.64 2.79 -0.15 2.00e-01 2.50e+01 5.50e-01 chirality pdb=" CB ILE H 54 " pdb=" CA ILE H 54 " pdb=" CG1 ILE H 54 " pdb=" CG2 ILE H 54 " both_signs ideal model delta sigma weight residual False 2.64 2.79 -0.15 2.00e-01 2.50e+01 5.30e-01 chirality pdb=" CB ILE D 54 " pdb=" CA ILE D 54 " pdb=" CG1 ILE D 54 " pdb=" CG2 ILE D 54 " both_signs ideal model delta sigma weight residual False 2.64 2.79 -0.15 2.00e-01 2.50e+01 5.29e-01 ... (remaining 351 not shown) Planarity restraints: 312 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL D 67 " -0.005 2.00e-02 2.50e+03 9.80e-03 9.60e-01 pdb=" C VAL D 67 " 0.017 2.00e-02 2.50e+03 pdb=" O VAL D 67 " -0.006 2.00e-02 2.50e+03 pdb=" N VAL D 68 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL J 67 " -0.005 2.00e-02 2.50e+03 9.64e-03 9.30e-01 pdb=" C VAL J 67 " 0.017 2.00e-02 2.50e+03 pdb=" O VAL J 67 " -0.006 2.00e-02 2.50e+03 pdb=" N VAL J 68 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 67 " -0.005 2.00e-02 2.50e+03 9.52e-03 9.07e-01 pdb=" C VAL B 67 " 0.016 2.00e-02 2.50e+03 pdb=" O VAL B 67 " -0.006 2.00e-02 2.50e+03 pdb=" N VAL B 68 " -0.006 2.00e-02 2.50e+03 ... (remaining 309 not shown) Histogram of nonbonded interaction distances: 2.53 - 3.01: 990 3.01 - 3.48: 1847 3.48 - 3.95: 2472 3.95 - 4.43: 3199 4.43 - 4.90: 5968 Nonbonded interactions: 14476 Sorted by model distance: nonbonded pdb=" OD1 ASN A 60 " pdb=" ND2 ASN C 60 " model vdw 2.534 3.120 nonbonded pdb=" OD1 ASN G 60 " pdb=" ND2 ASN I 60 " model vdw 2.534 3.120 nonbonded pdb=" ND2 ASN A 60 " pdb=" OD1 ASN E 60 " model vdw 2.561 3.120 nonbonded pdb=" ND2 ASN G 60 " pdb=" OD1 ASN K 60 " model vdw 2.562 3.120 nonbonded pdb=" N MET D 58 " pdb=" O MET D 58 " model vdw 2.623 2.496 ... (remaining 14471 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'K' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' selection = chain 'J' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.050 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.630 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7234 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 : 0.004 0.022 1932 Z= 0.194 Angle : 0.908 5.788 2586 Z= 0.457 Chirality : 0.044 0.148 354 Planarity : 0.002 0.010 312 Dihedral : 15.109 48.648 714 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 14.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.35 % Favored : 90.65 % Rotamer: Outliers : 0.00 % Allowed : 8.57 % Favored : 91.43 % 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: -6.23 (0.29), residues: 246 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.74 (0.22), residues: 246 Details of bonding type rmsd covalent geometry : bond 0.00390 ( 1932) covalent geometry : angle 0.90810 ( 2586) hydrogen bonds : bond 0.18541 ( 12) hydrogen bonds : angle 11.86009 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 57 time to evaluate : 0.115 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 69 GLU cc_start: 0.6835 (mm-30) cc_final: 0.6464 (mm-30) REVERT: D 65 LYS cc_start: 0.8008 (mttm) cc_final: 0.7806 (mttp) REVERT: E 52 LEU cc_start: 0.8352 (pp) cc_final: 0.8110 (pp) REVERT: E 58 MET cc_start: 0.7512 (mtm) cc_final: 0.7263 (mpp) REVERT: F 69 GLU cc_start: 0.7706 (mm-30) cc_final: 0.7399 (mm-30) REVERT: G 52 LEU cc_start: 0.8219 (pp) cc_final: 0.7943 (pp) REVERT: K 58 MET cc_start: 0.7704 (mtm) cc_final: 0.7404 (mpp) outliers start: 0 outliers final: 0 residues processed: 57 average time/residue: 0.0406 time to fit residues: 2.8164 Evaluate side-chains 51 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 51 time to evaluate : 0.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 12 optimal weight: 4.9990 chunk 13 optimal weight: 6.9990 chunk 1 optimal weight: 0.6980 chunk 8 optimal weight: 5.9990 chunk 16 optimal weight: 3.9990 chunk 15 optimal weight: 5.9990 chunk 9 optimal weight: 2.9990 chunk 11 optimal weight: 10.0000 chunk 18 optimal weight: 3.9990 chunk 6 optimal weight: 4.9990 chunk 4 optimal weight: 9.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 ASN C 60 ASN E 60 ASN G 60 ASN I 60 ASN K 60 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4738 r_free = 0.4738 target = 0.169110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4427 r_free = 0.4427 target = 0.135243 restraints weight = 1750.917| |-----------------------------------------------------------------------------| r_work (start): 0.4452 rms_B_bonded: 2.70 r_work: 0.4308 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.4174 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.4174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 moved from start: 0.1860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.045 1932 Z= 0.329 Angle : 1.094 8.927 2586 Z= 0.503 Chirality : 0.051 0.206 354 Planarity : 0.003 0.011 312 Dihedral : 5.587 18.006 258 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 21.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 19.51 % Favored : 80.49 % Rotamer: Outliers : 2.86 % Allowed : 22.86 % Favored : 74.29 % 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: -5.92 (0.32), residues: 246 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.51 (0.24), residues: 246 Details of bonding type rmsd covalent geometry : bond 0.00739 ( 1932) covalent geometry : angle 1.09376 ( 2586) hydrogen bonds : bond 0.04061 ( 12) hydrogen bonds : angle 10.20105 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 47 time to evaluate : 0.076 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 54 ILE cc_start: 0.8889 (OUTLIER) cc_final: 0.8689 (mp) REVERT: B 69 GLU cc_start: 0.6793 (mm-30) cc_final: 0.6203 (mm-30) REVERT: C 51 MET cc_start: 0.8269 (ptp) cc_final: 0.8038 (ptt) REVERT: C 58 MET cc_start: 0.8587 (mpp) cc_final: 0.8326 (mpp) REVERT: C 65 LYS cc_start: 0.7980 (tptp) cc_final: 0.7719 (tmtt) REVERT: D 69 GLU cc_start: 0.7471 (mm-30) cc_final: 0.7210 (mm-30) REVERT: F 69 GLU cc_start: 0.7629 (mm-30) cc_final: 0.7274 (mm-30) REVERT: G 52 LEU cc_start: 0.8567 (OUTLIER) cc_final: 0.8294 (pp) REVERT: H 51 MET cc_start: 0.7583 (ttp) cc_final: 0.6858 (ttp) REVERT: I 65 LYS cc_start: 0.8020 (tptp) cc_final: 0.7810 (tmtt) REVERT: J 51 MET cc_start: 0.7555 (ttp) cc_final: 0.7269 (ttp) REVERT: L 51 MET cc_start: 0.7704 (ttp) cc_final: 0.6936 (tpt) outliers start: 6 outliers final: 1 residues processed: 53 average time/residue: 0.0505 time to fit residues: 3.1254 Evaluate side-chains 50 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 47 time to evaluate : 0.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ILE Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 53 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 3 optimal weight: 10.0000 chunk 22 optimal weight: 0.9990 chunk 14 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- 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 = 0.4943 r_free = 0.4943 target = 0.195140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4665 r_free = 0.4665 target = 0.160283 restraints weight = 1699.625| |-----------------------------------------------------------------------------| r_work (start): 0.4712 rms_B_bonded: 2.81 r_work: 0.4524 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.4391 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.4391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7290 moved from start: 0.2196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 1932 Z= 0.168 Angle : 0.861 6.312 2586 Z= 0.413 Chirality : 0.049 0.167 354 Planarity : 0.002 0.011 312 Dihedral : 4.842 15.379 258 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 17.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 4.29 % Allowed : 21.43 % Favored : 74.29 % 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: -5.48 (0.34), residues: 246 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.17 (0.26), residues: 246 Details of bonding type rmsd covalent geometry : bond 0.00380 ( 1932) covalent geometry : angle 0.86118 ( 2586) hydrogen bonds : bond 0.04091 ( 12) hydrogen bonds : angle 10.06789 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 42 time to evaluate : 0.060 Fit side-chains REVERT: B 69 GLU cc_start: 0.6313 (mm-30) cc_final: 0.5888 (mm-30) REVERT: D 69 GLU cc_start: 0.7076 (mm-30) cc_final: 0.6794 (mm-30) REVERT: F 69 GLU cc_start: 0.7553 (mm-30) cc_final: 0.7206 (mm-30) REVERT: H 58 MET cc_start: 0.8256 (mtt) cc_final: 0.7972 (mtt) REVERT: J 51 MET cc_start: 0.7275 (ttp) cc_final: 0.7016 (ttp) REVERT: K 52 LEU cc_start: 0.8268 (OUTLIER) cc_final: 0.8025 (pp) REVERT: L 51 MET cc_start: 0.6775 (ttp) cc_final: 0.6209 (mmm) outliers start: 9 outliers final: 3 residues processed: 48 average time/residue: 0.0405 time to fit residues: 2.4155 Evaluate side-chains 46 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 42 time to evaluate : 0.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 54 ILE Chi-restraints excluded: chain I residue 58 MET Chi-restraints excluded: chain K residue 52 LEU Chi-restraints excluded: chain K residue 54 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 7 optimal weight: 8.9990 chunk 11 optimal weight: 4.9990 chunk 21 optimal weight: 0.9990 chunk 18 optimal weight: 4.9990 chunk 14 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 12 optimal weight: 9.9990 chunk 0 optimal weight: 7.9990 chunk 3 optimal weight: 0.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- 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 = 0.4916 r_free = 0.4916 target = 0.194826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4645 r_free = 0.4645 target = 0.160016 restraints weight = 1660.529| |-----------------------------------------------------------------------------| r_work (start): 0.4681 rms_B_bonded: 2.74 r_work: 0.4512 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.4382 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.4382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7321 moved from start: 0.2438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 1932 Z= 0.200 Angle : 0.870 7.000 2586 Z= 0.411 Chirality : 0.048 0.175 354 Planarity : 0.002 0.011 312 Dihedral : 4.740 15.008 258 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 19.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.38 % Favored : 88.62 % Rotamer: Outliers : 4.76 % Allowed : 22.38 % Favored : 72.86 % 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: -5.28 (0.34), residues: 246 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.02 (0.26), residues: 246 Details of bonding type rmsd covalent geometry : bond 0.00464 ( 1932) covalent geometry : angle 0.87039 ( 2586) hydrogen bonds : bond 0.03995 ( 12) hydrogen bonds : angle 10.04059 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 47 time to evaluate : 0.074 Fit side-chains REVERT: B 69 GLU cc_start: 0.6405 (mm-30) cc_final: 0.6176 (mm-30) REVERT: C 65 LYS cc_start: 0.7806 (tptp) cc_final: 0.7408 (tmtt) REVERT: D 51 MET cc_start: 0.7311 (ttp) cc_final: 0.6695 (ttp) REVERT: D 69 GLU cc_start: 0.7155 (mm-30) cc_final: 0.6878 (mm-30) REVERT: E 65 LYS cc_start: 0.8229 (tmtt) cc_final: 0.7976 (tmtt) REVERT: G 52 LEU cc_start: 0.8380 (OUTLIER) cc_final: 0.8098 (pp) REVERT: I 65 LYS cc_start: 0.8005 (tptp) cc_final: 0.7736 (tmtt) REVERT: K 52 LEU cc_start: 0.8385 (OUTLIER) cc_final: 0.8122 (pp) REVERT: K 58 MET cc_start: 0.7421 (OUTLIER) cc_final: 0.7146 (mpp) REVERT: K 65 LYS cc_start: 0.8535 (tmtt) cc_final: 0.8269 (tmtt) REVERT: L 51 MET cc_start: 0.7263 (ttp) cc_final: 0.6612 (mmm) REVERT: L 58 MET cc_start: 0.8107 (mtt) cc_final: 0.7819 (mtp) outliers start: 10 outliers final: 1 residues processed: 55 average time/residue: 0.0465 time to fit residues: 3.0396 Evaluate side-chains 49 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 45 time to evaluate : 0.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 54 ILE Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain K residue 52 LEU Chi-restraints excluded: chain K residue 58 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 11 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 18 optimal weight: 0.5980 chunk 8 optimal weight: 3.9990 chunk 4 optimal weight: 6.9990 chunk 16 optimal weight: 4.9990 chunk 5 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4870 r_free = 0.4870 target = 0.188631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4576 r_free = 0.4576 target = 0.153910 restraints weight = 1676.735| |-----------------------------------------------------------------------------| r_work (start): 0.4618 rms_B_bonded: 2.72 r_work: 0.4448 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.4318 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.4318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7376 moved from start: 0.2508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 1932 Z= 0.242 Angle : 0.959 9.076 2586 Z= 0.449 Chirality : 0.048 0.154 354 Planarity : 0.002 0.009 312 Dihedral : 4.952 15.919 258 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 20.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.16 % Favored : 89.84 % Rotamer: Outliers : 5.24 % Allowed : 24.29 % Favored : 70.48 % 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: -5.40 (0.34), residues: 246 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.11 (0.26), residues: 246 Details of bonding type rmsd covalent geometry : bond 0.00559 ( 1932) covalent geometry : angle 0.95886 ( 2586) hydrogen bonds : bond 0.03995 ( 12) hydrogen bonds : angle 10.11786 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 46 time to evaluate : 0.076 Fit side-chains REVERT: B 69 GLU cc_start: 0.6545 (mm-30) cc_final: 0.6137 (mm-30) REVERT: C 65 LYS cc_start: 0.7810 (tptp) cc_final: 0.7398 (tmtt) REVERT: D 69 GLU cc_start: 0.7082 (mm-30) cc_final: 0.6699 (mm-30) REVERT: E 65 LYS cc_start: 0.8304 (tmtt) cc_final: 0.8049 (tmtt) REVERT: F 51 MET cc_start: 0.7563 (ttp) cc_final: 0.7074 (mmm) REVERT: F 57 LEU cc_start: 0.7940 (mp) cc_final: 0.7626 (mt) REVERT: F 69 GLU cc_start: 0.7456 (mm-30) cc_final: 0.7171 (mm-30) REVERT: G 52 LEU cc_start: 0.8445 (OUTLIER) cc_final: 0.8172 (pp) REVERT: I 65 LYS cc_start: 0.7976 (tptp) cc_final: 0.7571 (tmtt) REVERT: K 52 LEU cc_start: 0.8497 (OUTLIER) cc_final: 0.8222 (pp) REVERT: K 65 LYS cc_start: 0.8616 (tmtt) cc_final: 0.8321 (tmtt) REVERT: L 51 MET cc_start: 0.7267 (ttp) cc_final: 0.6690 (mmm) outliers start: 11 outliers final: 2 residues processed: 55 average time/residue: 0.0466 time to fit residues: 3.0331 Evaluate side-chains 51 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 47 time to evaluate : 0.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 54 ILE Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain I residue 58 MET Chi-restraints excluded: chain K residue 52 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 3 optimal weight: 8.9990 chunk 17 optimal weight: 2.9990 chunk 12 optimal weight: 10.0000 chunk 8 optimal weight: 6.9990 chunk 20 optimal weight: 3.9990 chunk 6 optimal weight: 0.7980 chunk 5 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 7 optimal weight: 6.9990 chunk 18 optimal weight: 2.9990 chunk 2 optimal weight: 0.6980 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4892 r_free = 0.4892 target = 0.190743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4601 r_free = 0.4601 target = 0.156590 restraints weight = 1698.840| |-----------------------------------------------------------------------------| r_work (start): 0.4632 rms_B_bonded: 2.67 r_work: 0.4470 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.4345 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.4345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7362 moved from start: 0.2639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 1932 Z= 0.220 Angle : 0.921 8.896 2586 Z= 0.438 Chirality : 0.048 0.151 354 Planarity : 0.002 0.011 312 Dihedral : 4.874 19.820 258 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 19.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.76 % Favored : 90.24 % Rotamer: Outliers : 4.29 % Allowed : 25.71 % Favored : 70.00 % 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: -5.44 (0.34), residues: 246 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.14 (0.26), residues: 246 Details of bonding type rmsd covalent geometry : bond 0.00509 ( 1932) covalent geometry : angle 0.92097 ( 2586) hydrogen bonds : bond 0.03910 ( 12) hydrogen bonds : angle 9.98044 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 47 time to evaluate : 0.051 Fit side-chains REVERT: B 69 GLU cc_start: 0.6608 (mm-30) cc_final: 0.6148 (mm-30) REVERT: C 65 LYS cc_start: 0.7823 (tptp) cc_final: 0.7408 (tmtt) REVERT: D 69 GLU cc_start: 0.7194 (mm-30) cc_final: 0.6928 (mm-30) REVERT: E 65 LYS cc_start: 0.8291 (tmtt) cc_final: 0.8058 (tmtt) REVERT: F 51 MET cc_start: 0.7538 (ttp) cc_final: 0.7064 (mmm) REVERT: F 57 LEU cc_start: 0.7973 (mp) cc_final: 0.7652 (mt) REVERT: F 69 GLU cc_start: 0.7622 (mm-30) cc_final: 0.7261 (mm-30) REVERT: G 52 LEU cc_start: 0.8436 (OUTLIER) cc_final: 0.8184 (pp) REVERT: H 51 MET cc_start: 0.7167 (ttp) cc_final: 0.5809 (ttp) REVERT: I 65 LYS cc_start: 0.7990 (tptp) cc_final: 0.7579 (tmtt) REVERT: K 52 LEU cc_start: 0.8551 (OUTLIER) cc_final: 0.8232 (pp) REVERT: K 65 LYS cc_start: 0.8573 (tmtt) cc_final: 0.8250 (tmtt) REVERT: L 51 MET cc_start: 0.7238 (ttp) cc_final: 0.6684 (mmm) outliers start: 9 outliers final: 2 residues processed: 53 average time/residue: 0.0443 time to fit residues: 2.7805 Evaluate side-chains 49 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 45 time to evaluate : 0.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 54 ILE Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain I residue 58 MET Chi-restraints excluded: chain K residue 52 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 0 optimal weight: 9.9990 chunk 20 optimal weight: 0.0270 chunk 15 optimal weight: 8.9990 chunk 8 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 2 optimal weight: 3.9990 chunk 19 optimal weight: 10.0000 chunk 23 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 13 optimal weight: 0.6980 overall best weight: 1.3242 ------------------------------------------------------------------------------- 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 = 0.4970 r_free = 0.4970 target = 0.198700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4700 r_free = 0.4700 target = 0.164409 restraints weight = 1631.056| |-----------------------------------------------------------------------------| r_work (start): 0.4733 rms_B_bonded: 2.72 r_work: 0.4567 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.4440 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.4440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7269 moved from start: 0.2817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 1932 Z= 0.175 Angle : 0.882 9.322 2586 Z= 0.422 Chirality : 0.050 0.200 354 Planarity : 0.002 0.009 312 Dihedral : 4.499 15.269 258 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 17.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.32 % Favored : 92.68 % Rotamer: Outliers : 4.76 % Allowed : 26.67 % Favored : 68.57 % 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: -5.36 (0.34), residues: 246 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.08 (0.26), residues: 246 Details of bonding type rmsd covalent geometry : bond 0.00401 ( 1932) covalent geometry : angle 0.88215 ( 2586) hydrogen bonds : bond 0.03872 ( 12) hydrogen bonds : angle 9.72126 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 52 time to evaluate : 0.045 Fit side-chains REVERT: B 58 MET cc_start: 0.7628 (mtt) cc_final: 0.7332 (mtt) REVERT: B 69 GLU cc_start: 0.6632 (mm-30) cc_final: 0.6184 (mm-30) REVERT: C 65 LYS cc_start: 0.7796 (tptp) cc_final: 0.7379 (tmtt) REVERT: D 69 GLU cc_start: 0.7137 (mm-30) cc_final: 0.6866 (mm-30) REVERT: E 65 LYS cc_start: 0.8253 (tmtt) cc_final: 0.8025 (tmtt) REVERT: F 51 MET cc_start: 0.7469 (ttp) cc_final: 0.6990 (mmm) REVERT: F 57 LEU cc_start: 0.8017 (mp) cc_final: 0.7732 (mt) REVERT: F 69 GLU cc_start: 0.7552 (mm-30) cc_final: 0.7183 (mm-30) REVERT: G 52 LEU cc_start: 0.8369 (OUTLIER) cc_final: 0.8117 (pp) REVERT: G 58 MET cc_start: 0.7516 (mtp) cc_final: 0.7256 (mtp) REVERT: K 52 LEU cc_start: 0.8524 (OUTLIER) cc_final: 0.8184 (pp) REVERT: K 65 LYS cc_start: 0.8523 (tmtt) cc_final: 0.8220 (tmtt) REVERT: L 51 MET cc_start: 0.7070 (ttp) cc_final: 0.6584 (mmm) outliers start: 10 outliers final: 3 residues processed: 59 average time/residue: 0.0351 time to fit residues: 2.4515 Evaluate side-chains 55 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 50 time to evaluate : 0.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain I residue 54 ILE Chi-restraints excluded: chain J residue 54 ILE Chi-restraints excluded: chain K residue 52 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 8 optimal weight: 0.2980 chunk 19 optimal weight: 7.9990 chunk 13 optimal weight: 0.6980 chunk 4 optimal weight: 9.9990 chunk 22 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 chunk 6 optimal weight: 0.0980 chunk 0 optimal weight: 0.7980 chunk 23 optimal weight: 7.9990 chunk 5 optimal weight: 2.9990 chunk 17 optimal weight: 7.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5038 r_free = 0.5038 target = 0.201646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4831 r_free = 0.4831 target = 0.170801 restraints weight = 1659.365| |-----------------------------------------------------------------------------| r_work (start): 0.4844 rms_B_bonded: 2.75 r_work: 0.4718 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.4590 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.4590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7008 moved from start: 0.3284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 1932 Z= 0.129 Angle : 0.898 8.802 2586 Z= 0.426 Chirality : 0.052 0.220 354 Planarity : 0.002 0.012 312 Dihedral : 3.934 12.588 258 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 15.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 2.86 % Allowed : 29.52 % Favored : 67.62 % 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: -5.04 (0.36), residues: 246 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.83 (0.27), residues: 246 Details of bonding type rmsd covalent geometry : bond 0.00273 ( 1932) covalent geometry : angle 0.89796 ( 2586) hydrogen bonds : bond 0.03708 ( 12) hydrogen bonds : angle 9.46743 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 53 time to evaluate : 0.047 Fit side-chains REVERT: B 69 GLU cc_start: 0.6503 (mm-30) cc_final: 0.6150 (mm-30) REVERT: C 58 MET cc_start: 0.8493 (mpp) cc_final: 0.8282 (mpp) REVERT: D 51 MET cc_start: 0.7069 (ttp) cc_final: 0.6478 (ttp) REVERT: E 65 LYS cc_start: 0.8199 (tmtt) cc_final: 0.7954 (tmtt) REVERT: F 51 MET cc_start: 0.7167 (ttp) cc_final: 0.6641 (mmm) REVERT: F 57 LEU cc_start: 0.7744 (mp) cc_final: 0.7541 (mt) REVERT: F 69 GLU cc_start: 0.7542 (mm-30) cc_final: 0.7274 (mm-30) REVERT: G 52 LEU cc_start: 0.8309 (OUTLIER) cc_final: 0.8072 (pp) REVERT: K 52 LEU cc_start: 0.8160 (OUTLIER) cc_final: 0.7805 (pp) REVERT: K 65 LYS cc_start: 0.8445 (tmtt) cc_final: 0.8172 (tmtt) outliers start: 6 outliers final: 1 residues processed: 56 average time/residue: 0.0433 time to fit residues: 2.8704 Evaluate side-chains 54 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 51 time to evaluate : 0.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain K residue 52 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 8 optimal weight: 0.2980 chunk 20 optimal weight: 5.9990 chunk 18 optimal weight: 4.9990 chunk 23 optimal weight: 8.9990 chunk 19 optimal weight: 7.9990 chunk 17 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 13 optimal weight: 0.0060 chunk 5 optimal weight: 3.9990 chunk 22 optimal weight: 0.0070 chunk 7 optimal weight: 3.9990 overall best weight: 1.2618 ------------------------------------------------------------------------------- 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 = 0.4961 r_free = 0.4961 target = 0.191883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4713 r_free = 0.4713 target = 0.159901 restraints weight = 1690.477| |-----------------------------------------------------------------------------| r_work (start): 0.4718 rms_B_bonded: 2.75 r_work: 0.4583 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.4451 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.4451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7053 moved from start: 0.3195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 1932 Z= 0.175 Angle : 0.930 8.836 2586 Z= 0.438 Chirality : 0.052 0.213 354 Planarity : 0.002 0.010 312 Dihedral : 4.239 14.412 258 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 17.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.91 % Favored : 93.09 % Rotamer: Outliers : 4.29 % Allowed : 27.62 % Favored : 68.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.02 (0.36), residues: 246 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.82 (0.28), residues: 246 Details of bonding type rmsd covalent geometry : bond 0.00401 ( 1932) covalent geometry : angle 0.93043 ( 2586) hydrogen bonds : bond 0.03649 ( 12) hydrogen bonds : angle 9.74584 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 48 time to evaluate : 0.051 Fit side-chains REVERT: B 69 GLU cc_start: 0.6416 (mm-30) cc_final: 0.6154 (mm-30) REVERT: C 65 LYS cc_start: 0.7738 (tptp) cc_final: 0.7283 (tmtt) REVERT: E 65 LYS cc_start: 0.8210 (tmtt) cc_final: 0.7964 (tmtt) REVERT: F 51 MET cc_start: 0.7448 (ttp) cc_final: 0.6966 (mmm) REVERT: F 57 LEU cc_start: 0.8008 (mp) cc_final: 0.7761 (mt) REVERT: F 69 GLU cc_start: 0.7536 (mm-30) cc_final: 0.7331 (mm-30) REVERT: G 52 LEU cc_start: 0.8410 (OUTLIER) cc_final: 0.8170 (pp) REVERT: K 52 LEU cc_start: 0.8367 (OUTLIER) cc_final: 0.8025 (pp) REVERT: K 58 MET cc_start: 0.7318 (ptm) cc_final: 0.6856 (ptp) REVERT: K 65 LYS cc_start: 0.8537 (tmtt) cc_final: 0.8277 (tmtt) outliers start: 9 outliers final: 6 residues processed: 56 average time/residue: 0.0314 time to fit residues: 2.0920 Evaluate side-chains 56 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 48 time to evaluate : 0.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain E residue 54 ILE Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 54 ILE Chi-restraints excluded: chain I residue 54 ILE Chi-restraints excluded: chain K residue 52 LEU Chi-restraints excluded: chain K residue 54 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 17 optimal weight: 3.9990 chunk 0 optimal weight: 9.9990 chunk 12 optimal weight: 10.0000 chunk 14 optimal weight: 6.9990 chunk 7 optimal weight: 6.9990 chunk 21 optimal weight: 4.9990 chunk 5 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 chunk 19 optimal weight: 6.9990 chunk 6 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4868 r_free = 0.4868 target = 0.186042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4582 r_free = 0.4582 target = 0.153328 restraints weight = 1777.480| |-----------------------------------------------------------------------------| r_work (start): 0.4592 rms_B_bonded: 2.60 r_work: 0.4430 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.4306 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.4306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7429 moved from start: 0.2948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.051 1932 Z= 0.326 Angle : 1.137 10.131 2586 Z= 0.523 Chirality : 0.053 0.227 354 Planarity : 0.002 0.011 312 Dihedral : 5.074 18.379 258 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 19.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.67 % Favored : 83.33 % Rotamer: Outliers : 3.81 % Allowed : 29.05 % Favored : 67.14 % 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: -5.52 (0.34), residues: 246 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.20 (0.26), residues: 246 Details of bonding type rmsd covalent geometry : bond 0.00762 ( 1932) covalent geometry : angle 1.13745 ( 2586) hydrogen bonds : bond 0.04169 ( 12) hydrogen bonds : angle 10.24280 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 50 time to evaluate : 0.044 Fit side-chains REVERT: B 69 GLU cc_start: 0.6969 (mm-30) cc_final: 0.6723 (mm-30) REVERT: C 65 LYS cc_start: 0.7872 (tptp) cc_final: 0.7519 (tmtt) REVERT: D 51 MET cc_start: 0.7208 (ttp) cc_final: 0.6596 (ttp) REVERT: D 69 GLU cc_start: 0.7132 (mm-30) cc_final: 0.6795 (mm-30) REVERT: E 52 LEU cc_start: 0.8552 (pp) cc_final: 0.8338 (pp) REVERT: E 65 LYS cc_start: 0.8340 (tmtt) cc_final: 0.8104 (tmtt) REVERT: F 51 MET cc_start: 0.7719 (ttp) cc_final: 0.7231 (mmm) REVERT: G 52 LEU cc_start: 0.8539 (OUTLIER) cc_final: 0.8257 (pp) REVERT: I 65 LYS cc_start: 0.8052 (tptp) cc_final: 0.7613 (tmtt) REVERT: J 51 MET cc_start: 0.6981 (ttp) cc_final: 0.5433 (tpt) REVERT: K 52 LEU cc_start: 0.8668 (OUTLIER) cc_final: 0.8345 (pp) REVERT: K 65 LYS cc_start: 0.8690 (tmtt) cc_final: 0.8420 (tmtt) outliers start: 8 outliers final: 4 residues processed: 57 average time/residue: 0.0337 time to fit residues: 2.2590 Evaluate side-chains 55 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 49 time to evaluate : 0.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain E residue 54 ILE Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 54 ILE Chi-restraints excluded: chain K residue 52 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 15 optimal weight: 7.9990 chunk 13 optimal weight: 0.6980 chunk 19 optimal weight: 3.9990 chunk 18 optimal weight: 0.9990 chunk 8 optimal weight: 6.9990 chunk 7 optimal weight: 5.9990 chunk 23 optimal weight: 3.9990 chunk 16 optimal weight: 6.9990 chunk 0 optimal weight: 0.9980 chunk 20 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- 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 = 0.4923 r_free = 0.4923 target = 0.192734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4641 r_free = 0.4641 target = 0.159826 restraints weight = 1739.459| |-----------------------------------------------------------------------------| r_work (start): 0.4660 rms_B_bonded: 2.70 r_work: 0.4500 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.4369 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.4369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7340 moved from start: 0.3045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 1932 Z= 0.239 Angle : 1.078 9.732 2586 Z= 0.499 Chirality : 0.053 0.222 354 Planarity : 0.002 0.011 312 Dihedral : 4.865 18.408 258 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 19.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.54 % Favored : 91.46 % Rotamer: Outliers : 2.86 % Allowed : 29.52 % Favored : 67.62 % 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: -5.53 (0.34), residues: 246 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.21 (0.26), residues: 246 Details of bonding type rmsd covalent geometry : bond 0.00562 ( 1932) covalent geometry : angle 1.07761 ( 2586) hydrogen bonds : bond 0.03847 ( 12) hydrogen bonds : angle 9.95873 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 641.12 seconds wall clock time: 11 minutes 34.97 seconds (694.97 seconds total)