Starting phenix.real_space_refine on Tue Mar 3 21:11:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9xb1_66695/03_2026/9xb1_66695_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9xb1_66695/03_2026/9xb1_66695.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9xb1_66695/03_2026/9xb1_66695_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9xb1_66695/03_2026/9xb1_66695_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9xb1_66695/03_2026/9xb1_66695.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9xb1_66695/03_2026/9xb1_66695.map" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.025 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 46 5.16 5 C 2796 2.51 5 N 678 2.21 5 O 664 1.98 5 H 4140 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8324 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 4134 Classifications: {'peptide': 256} Link IDs: {'PTRANS': 11, 'TRANS': 244} Chain breaks: 5 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: B Time building chain proxies: 2.71, per 1000 atoms: 0.33 Number of scatterers: 8324 At special positions: 0 Unit cell: (91.08, 85.56, 73.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 46 16.00 O 664 8.00 N 678 7.00 C 2796 6.00 H 4140 1.00 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: 0.76 Conformation dependent library (CDL) restraints added in 170.4 milliseconds 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 988 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 0 sheets defined 87.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.16 Creating SS restraints... Processing helix chain 'A' and resid 47 through 78 Processing helix chain 'A' and resid 85 through 104 removed outlier: 3.851A pdb=" N PHE A 89 " --> pdb=" O ARG A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 114 Processing helix chain 'A' and resid 120 through 155 removed outlier: 3.820A pdb=" N LEU A 142 " --> pdb=" O SER A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 183 Processing helix chain 'A' and resid 183 through 188 Processing helix chain 'A' and resid 203 through 207 Processing helix chain 'A' and resid 213 through 225 Processing helix chain 'A' and resid 225 through 246 Processing helix chain 'A' and resid 283 through 317 Proline residue: A 306 - end of helix Processing helix chain 'A' and resid 328 through 338 Processing helix chain 'A' and resid 339 through 351 removed outlier: 3.842A pdb=" N LYS A 344 " --> pdb=" O ASN A 340 " (cutoff:3.500A) Proline residue: A 345 - end of helix Processing helix chain 'B' and resid 47 through 78 Processing helix chain 'B' and resid 85 through 104 removed outlier: 3.852A pdb=" N PHE B 89 " --> pdb=" O ARG B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 114 Processing helix chain 'B' and resid 120 through 155 removed outlier: 3.821A pdb=" N LEU B 142 " --> pdb=" O SER B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 163 through 183 Processing helix chain 'B' and resid 183 through 188 Processing helix chain 'B' and resid 203 through 207 Processing helix chain 'B' and resid 213 through 225 Processing helix chain 'B' and resid 225 through 246 Processing helix chain 'B' and resid 283 through 317 Proline residue: B 306 - end of helix Processing helix chain 'B' and resid 328 through 338 Processing helix chain 'B' and resid 339 through 351 removed outlier: 3.842A pdb=" N LYS B 344 " --> pdb=" O ASN B 340 " (cutoff:3.500A) Proline residue: B 345 - end of helix 336 hydrogen bonds defined for protein. 996 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: 1.76 Time building geometry restraints manager: 1.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 4118 1.03 - 1.23: 22 1.23 - 1.42: 1836 1.42 - 1.62: 2406 1.62 - 1.81: 70 Bond restraints: 8452 Sorted by residual: bond pdb=" CA ARG B 46 " pdb=" CB ARG B 46 " ideal model delta sigma weight residual 1.530 1.542 -0.012 1.69e-02 3.50e+03 4.68e-01 bond pdb=" CA ARG A 46 " pdb=" CB ARG A 46 " ideal model delta sigma weight residual 1.530 1.541 -0.011 1.69e-02 3.50e+03 4.43e-01 bond pdb=" CA THR B 183 " pdb=" C THR B 183 " ideal model delta sigma weight residual 1.522 1.530 -0.008 1.29e-02 6.01e+03 4.21e-01 bond pdb=" CG PRO A 228 " pdb=" CD PRO A 228 " ideal model delta sigma weight residual 1.503 1.482 0.021 3.40e-02 8.65e+02 3.77e-01 bond pdb=" CA THR A 183 " pdb=" C THR A 183 " ideal model delta sigma weight residual 1.522 1.529 -0.008 1.29e-02 6.01e+03 3.69e-01 ... (remaining 8447 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.07: 14188 1.07 - 2.13: 932 2.13 - 3.20: 46 3.20 - 4.26: 6 4.26 - 5.33: 10 Bond angle restraints: 15182 Sorted by residual: angle pdb=" N ILE A 224 " pdb=" CA ILE A 224 " pdb=" C ILE A 224 " ideal model delta sigma weight residual 112.96 110.22 2.74 1.00e+00 1.00e+00 7.49e+00 angle pdb=" N ILE B 224 " pdb=" CA ILE B 224 " pdb=" C ILE B 224 " ideal model delta sigma weight residual 112.96 110.26 2.70 1.00e+00 1.00e+00 7.31e+00 angle pdb=" C VAL A 45 " pdb=" N ARG A 46 " pdb=" CA ARG A 46 " ideal model delta sigma weight residual 121.54 126.57 -5.03 1.91e+00 2.74e-01 6.94e+00 angle pdb=" C VAL B 45 " pdb=" N ARG B 46 " pdb=" CA ARG B 46 " ideal model delta sigma weight residual 121.54 126.49 -4.95 1.91e+00 2.74e-01 6.71e+00 angle pdb=" N VAL B 188 " pdb=" CA VAL B 188 " pdb=" C VAL B 188 " ideal model delta sigma weight residual 112.12 110.49 1.63 8.40e-01 1.42e+00 3.75e+00 ... (remaining 15177 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.10: 3641 15.10 - 30.20: 307 30.20 - 45.29: 102 45.29 - 60.39: 48 60.39 - 75.49: 8 Dihedral angle restraints: 4106 sinusoidal: 2174 harmonic: 1932 Sorted by residual: dihedral pdb=" N ARG A 46 " pdb=" CA ARG A 46 " pdb=" CB ARG A 46 " pdb=" CG ARG A 46 " ideal model delta sinusoidal sigma weight residual -60.00 -119.44 59.44 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" N ARG B 46 " pdb=" CA ARG B 46 " pdb=" CB ARG B 46 " pdb=" CG ARG B 46 " ideal model delta sinusoidal sigma weight residual -60.00 -119.41 59.41 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" CB MET A 349 " pdb=" CG MET A 349 " pdb=" SD MET A 349 " pdb=" CE MET A 349 " ideal model delta sinusoidal sigma weight residual -60.00 -2.18 -57.82 3 1.50e+01 4.44e-03 9.45e+00 ... (remaining 4103 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.023: 414 0.023 - 0.046: 116 0.046 - 0.069: 90 0.069 - 0.092: 53 0.092 - 0.115: 7 Chirality restraints: 680 Sorted by residual: chirality pdb=" CA ILE A 282 " pdb=" N ILE A 282 " pdb=" C ILE A 282 " pdb=" CB ILE A 282 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.33e-01 chirality pdb=" CA ILE B 282 " pdb=" N ILE B 282 " pdb=" C ILE B 282 " pdb=" CB ILE B 282 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.11 2.00e-01 2.50e+01 3.27e-01 chirality pdb=" CA PRO B 318 " pdb=" N PRO B 318 " pdb=" C PRO B 318 " pdb=" CB PRO B 318 " both_signs ideal model delta sigma weight residual False 2.72 2.62 0.10 2.00e-01 2.50e+01 2.48e-01 ... (remaining 677 not shown) Planarity restraints: 1160 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA B 227 " 0.019 5.00e-02 4.00e+02 2.90e-02 1.35e+00 pdb=" N PRO B 228 " -0.050 5.00e-02 4.00e+02 pdb=" CA PRO B 228 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO B 228 " 0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 227 " -0.019 5.00e-02 4.00e+02 2.89e-02 1.33e+00 pdb=" N PRO A 228 " 0.050 5.00e-02 4.00e+02 pdb=" CA PRO A 228 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 228 " -0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 344 " -0.014 5.00e-02 4.00e+02 2.10e-02 7.02e-01 pdb=" N PRO A 345 " 0.036 5.00e-02 4.00e+02 pdb=" CA PRO A 345 " -0.011 5.00e-02 4.00e+02 pdb=" CD PRO A 345 " -0.012 5.00e-02 4.00e+02 ... (remaining 1157 not shown) Histogram of nonbonded interaction distances: 1.65 - 2.24: 836 2.24 - 2.83: 18477 2.83 - 3.42: 23091 3.42 - 4.01: 31042 4.01 - 4.60: 47685 Nonbonded interactions: 121131 Sorted by model distance: nonbonded pdb="HH21 ARG B 85 " pdb=" OD1 ASP B 148 " model vdw 1.655 2.450 nonbonded pdb="HH21 ARG A 85 " pdb=" OD1 ASP A 148 " model vdw 1.655 2.450 nonbonded pdb=" HZ1 LYS B 128 " pdb=" O TRP B 204 " model vdw 1.765 2.450 nonbonded pdb=" HZ1 LYS A 128 " pdb=" O TRP A 204 " model vdw 1.765 2.450 nonbonded pdb=" O THR A 221 " pdb=" H VAL A 226 " model vdw 1.771 2.450 ... (remaining 121126 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 'B' } 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: 2.260 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: 0.050 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.970 Find NCS groups from input model: 0.030 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:6.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 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 : 0.002 0.027 4312 Z= 0.106 Angle : 0.492 5.330 5884 Z= 0.275 Chirality : 0.036 0.115 680 Planarity : 0.003 0.029 686 Dihedral : 14.740 75.487 1578 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 0.45 % Allowed : 15.25 % Favored : 84.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.31 (0.38), residues: 488 helix: 1.97 (0.25), residues: 420 sheet: None (None), residues: 0 loop : -1.30 (0.77), residues: 68 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 166 TYR 0.007 0.001 TYR B 236 PHE 0.004 0.001 PHE B 207 TRP 0.011 0.001 TRP A 219 HIS 0.002 0.000 HIS A 92 Details of bonding type rmsd covalent geometry : bond 0.00215 ( 4312) covalent geometry : angle 0.49233 ( 5884) hydrogen bonds : bond 0.11743 ( 336) hydrogen bonds : angle 5.65051 ( 996) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 48 time to evaluate : 0.213 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 48 average time/residue: 1.0559 time to fit residues: 52.6653 Evaluate side-chains 46 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 24 optimal weight: 0.7980 chunk 48 optimal weight: 0.8980 chunk 26 optimal weight: 0.8980 chunk 2 optimal weight: 0.1980 chunk 16 optimal weight: 0.0770 chunk 32 optimal weight: 0.5980 chunk 31 optimal weight: 0.5980 chunk 25 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 30 optimal weight: 0.1980 chunk 22 optimal weight: 2.9990 overall best weight: 0.3338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 209 GLN B 209 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.156784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.127030 restraints weight = 11644.130| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 1.58 r_work: 0.3312 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3167 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.1089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4312 Z= 0.126 Angle : 0.475 5.081 5884 Z= 0.240 Chirality : 0.036 0.112 680 Planarity : 0.004 0.025 686 Dihedral : 4.950 40.518 676 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 0.90 % Allowed : 14.80 % Favored : 84.30 % 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: 3.23 (0.37), residues: 488 helix: 2.62 (0.24), residues: 420 sheet: None (None), residues: 0 loop : -1.19 (0.75), residues: 68 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 166 TYR 0.015 0.001 TYR A 236 PHE 0.011 0.001 PHE B 189 TRP 0.008 0.001 TRP A 346 HIS 0.006 0.001 HIS A 92 Details of bonding type rmsd covalent geometry : bond 0.00284 ( 4312) covalent geometry : angle 0.47465 ( 5884) hydrogen bonds : bond 0.03516 ( 336) hydrogen bonds : angle 4.24759 ( 996) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 58 time to evaluate : 0.208 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 141 MET cc_start: 0.8696 (mmm) cc_final: 0.8331 (tpp) REVERT: A 206 THR cc_start: 0.7787 (m) cc_final: 0.7223 (p) REVERT: B 165 ARG cc_start: 0.7407 (tpt-90) cc_final: 0.7109 (tpt170) REVERT: B 206 THR cc_start: 0.7767 (m) cc_final: 0.7198 (p) outliers start: 4 outliers final: 2 residues processed: 62 average time/residue: 0.9412 time to fit residues: 60.8474 Evaluate side-chains 56 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 54 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain B residue 315 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 15 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 chunk 22 optimal weight: 0.9990 chunk 21 optimal weight: 0.3980 chunk 43 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 14 optimal weight: 0.6980 chunk 48 optimal weight: 0.9990 chunk 37 optimal weight: 0.9990 chunk 2 optimal weight: 0.9990 chunk 42 optimal weight: 0.4980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 209 GLN B 209 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.149653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.117601 restraints weight = 11820.059| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 1.71 r_work: 0.3197 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3052 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.1814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 4312 Z= 0.190 Angle : 0.507 4.979 5884 Z= 0.264 Chirality : 0.037 0.114 680 Planarity : 0.005 0.037 686 Dihedral : 5.238 39.507 676 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.57 % Allowed : 15.92 % Favored : 82.51 % 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: 3.01 (0.37), residues: 488 helix: 2.42 (0.24), residues: 422 sheet: None (None), residues: 0 loop : -1.00 (0.78), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 85 TYR 0.020 0.002 TYR B 236 PHE 0.008 0.001 PHE B 189 TRP 0.010 0.001 TRP A 346 HIS 0.006 0.001 HIS B 92 Details of bonding type rmsd covalent geometry : bond 0.00442 ( 4312) covalent geometry : angle 0.50689 ( 5884) hydrogen bonds : bond 0.03861 ( 336) hydrogen bonds : angle 4.41651 ( 996) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 53 time to evaluate : 0.214 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 206 THR cc_start: 0.7813 (m) cc_final: 0.7266 (p) REVERT: B 169 LEU cc_start: 0.8333 (mm) cc_final: 0.8095 (mp) REVERT: B 206 THR cc_start: 0.7780 (m) cc_final: 0.7224 (p) outliers start: 7 outliers final: 5 residues processed: 60 average time/residue: 0.8622 time to fit residues: 54.0880 Evaluate side-chains 57 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 52 time to evaluate : 0.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 GLN Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain B residue 85 ARG Chi-restraints excluded: chain B residue 131 GLN Chi-restraints excluded: chain B residue 315 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 29 optimal weight: 0.9990 chunk 43 optimal weight: 0.0270 chunk 14 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 48 optimal weight: 0.1980 chunk 39 optimal weight: 0.9980 chunk 42 optimal weight: 0.9980 chunk 8 optimal weight: 0.9990 chunk 13 optimal weight: 0.5980 chunk 7 optimal weight: 0.9990 chunk 25 optimal weight: 0.9980 overall best weight: 0.5638 ------------------------------------------------------------------------------- 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 = 0.4018 r_free = 0.4018 target = 0.161924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.131278 restraints weight = 12864.502| |-----------------------------------------------------------------------------| r_work (start): 0.3678 rms_B_bonded: 1.85 r_work: 0.3581 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3469 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7397 moved from start: 0.2085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 4312 Z= 0.160 Angle : 0.476 4.859 5884 Z= 0.246 Chirality : 0.036 0.114 680 Planarity : 0.004 0.034 686 Dihedral : 5.155 39.298 676 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.35 % Allowed : 15.02 % Favored : 83.63 % 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: 3.12 (0.37), residues: 488 helix: 2.51 (0.24), residues: 422 sheet: None (None), residues: 0 loop : -1.06 (0.78), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 149 TYR 0.016 0.002 TYR B 236 PHE 0.009 0.001 PHE B 350 TRP 0.009 0.001 TRP A 346 HIS 0.005 0.001 HIS A 92 Details of bonding type rmsd covalent geometry : bond 0.00365 ( 4312) covalent geometry : angle 0.47620 ( 5884) hydrogen bonds : bond 0.03649 ( 336) hydrogen bonds : angle 4.32897 ( 996) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 57 time to evaluate : 0.224 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 169 LEU cc_start: 0.7937 (mm) cc_final: 0.7685 (mp) REVERT: A 206 THR cc_start: 0.7353 (m) cc_final: 0.6692 (p) REVERT: B 206 THR cc_start: 0.7379 (m) cc_final: 0.6740 (p) outliers start: 6 outliers final: 5 residues processed: 63 average time/residue: 0.9069 time to fit residues: 59.8293 Evaluate side-chains 55 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 50 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 GLN Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain B residue 85 ARG Chi-restraints excluded: chain B residue 131 GLN Chi-restraints excluded: chain B residue 315 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 1 optimal weight: 0.9990 chunk 21 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 chunk 46 optimal weight: 0.7980 chunk 12 optimal weight: 0.9980 chunk 27 optimal weight: 0.6980 chunk 33 optimal weight: 0.9980 chunk 19 optimal weight: 0.9980 chunk 5 optimal weight: 0.3980 chunk 13 optimal weight: 1.9990 chunk 29 optimal weight: 0.1980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 209 GLN B 209 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.160170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.130002 restraints weight = 12787.024| |-----------------------------------------------------------------------------| r_work (start): 0.3672 rms_B_bonded: 1.80 r_work: 0.3574 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3464 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7414 moved from start: 0.2148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 4312 Z= 0.170 Angle : 0.488 4.931 5884 Z= 0.251 Chirality : 0.037 0.115 680 Planarity : 0.004 0.035 686 Dihedral : 5.119 37.357 676 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.69 % Allowed : 13.90 % Favored : 83.41 % 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: 3.07 (0.36), residues: 488 helix: 2.48 (0.23), residues: 422 sheet: None (None), residues: 0 loop : -1.11 (0.77), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 85 TYR 0.017 0.002 TYR A 236 PHE 0.006 0.001 PHE A 225 TRP 0.009 0.001 TRP A 219 HIS 0.006 0.001 HIS B 92 Details of bonding type rmsd covalent geometry : bond 0.00393 ( 4312) covalent geometry : angle 0.48831 ( 5884) hydrogen bonds : bond 0.03696 ( 336) hydrogen bonds : angle 4.36174 ( 996) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 51 time to evaluate : 0.206 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 206 THR cc_start: 0.7337 (m) cc_final: 0.6716 (p) REVERT: B 169 LEU cc_start: 0.7752 (mm) cc_final: 0.7520 (mp) REVERT: B 206 THR cc_start: 0.7363 (m) cc_final: 0.6750 (p) outliers start: 12 outliers final: 5 residues processed: 63 average time/residue: 1.0036 time to fit residues: 65.6711 Evaluate side-chains 56 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 51 time to evaluate : 0.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 GLN Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain B residue 85 ARG Chi-restraints excluded: chain B residue 131 GLN Chi-restraints excluded: chain B residue 315 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 32 optimal weight: 0.7980 chunk 9 optimal weight: 0.9990 chunk 6 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 43 optimal weight: 0.0050 chunk 4 optimal weight: 0.5980 chunk 3 optimal weight: 0.9980 chunk 44 optimal weight: 0.3980 chunk 38 optimal weight: 1.9990 chunk 40 optimal weight: 0.5980 chunk 14 optimal weight: 0.6980 overall best weight: 0.4594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 209 GLN B 209 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.161317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.131163 restraints weight = 12569.847| |-----------------------------------------------------------------------------| r_work (start): 0.3693 rms_B_bonded: 1.79 r_work: 0.3595 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3485 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7414 moved from start: 0.2355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4312 Z= 0.143 Angle : 0.471 5.560 5884 Z= 0.242 Chirality : 0.036 0.116 680 Planarity : 0.004 0.036 686 Dihedral : 5.047 36.679 676 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.57 % Allowed : 14.57 % Favored : 83.86 % 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: 3.27 (0.37), residues: 488 helix: 2.62 (0.24), residues: 422 sheet: None (None), residues: 0 loop : -1.07 (0.77), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 85 TYR 0.015 0.002 TYR A 236 PHE 0.011 0.001 PHE B 350 TRP 0.010 0.001 TRP B 219 HIS 0.005 0.001 HIS B 92 Details of bonding type rmsd covalent geometry : bond 0.00321 ( 4312) covalent geometry : angle 0.47147 ( 5884) hydrogen bonds : bond 0.03578 ( 336) hydrogen bonds : angle 4.27553 ( 996) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 52 time to evaluate : 0.219 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 169 LEU cc_start: 0.7953 (mm) cc_final: 0.7680 (mp) REVERT: A 206 THR cc_start: 0.7361 (m) cc_final: 0.6736 (p) REVERT: B 169 LEU cc_start: 0.7806 (mm) cc_final: 0.7564 (mp) REVERT: B 206 THR cc_start: 0.7353 (m) cc_final: 0.6737 (p) outliers start: 7 outliers final: 5 residues processed: 59 average time/residue: 0.9261 time to fit residues: 56.9913 Evaluate side-chains 57 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 52 time to evaluate : 0.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 GLN Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain B residue 85 ARG Chi-restraints excluded: chain B residue 131 GLN Chi-restraints excluded: chain B residue 315 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 3 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 33 optimal weight: 0.9990 chunk 29 optimal weight: 0.9990 chunk 24 optimal weight: 0.4980 chunk 21 optimal weight: 0.9980 chunk 36 optimal weight: 0.3980 chunk 17 optimal weight: 0.9990 chunk 1 optimal weight: 0.5980 chunk 15 optimal weight: 0.3980 chunk 10 optimal weight: 0.6980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 209 GLN B 209 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.160619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.130338 restraints weight = 12939.128| |-----------------------------------------------------------------------------| r_work (start): 0.3682 rms_B_bonded: 1.83 r_work: 0.3585 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3474 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7412 moved from start: 0.2323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 4312 Z= 0.155 Angle : 0.483 6.124 5884 Z= 0.247 Chirality : 0.036 0.116 680 Planarity : 0.004 0.037 686 Dihedral : 5.033 35.645 676 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 1.57 % Allowed : 14.57 % Favored : 83.86 % 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: 3.23 (0.37), residues: 488 helix: 2.59 (0.24), residues: 422 sheet: None (None), residues: 0 loop : -1.07 (0.76), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 85 TYR 0.016 0.002 TYR A 236 PHE 0.005 0.001 PHE A 225 TRP 0.015 0.001 TRP B 219 HIS 0.005 0.001 HIS A 92 Details of bonding type rmsd covalent geometry : bond 0.00354 ( 4312) covalent geometry : angle 0.48263 ( 5884) hydrogen bonds : bond 0.03600 ( 336) hydrogen bonds : angle 4.27492 ( 996) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 55 time to evaluate : 0.174 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 169 LEU cc_start: 0.7966 (mm) cc_final: 0.7699 (mp) REVERT: A 206 THR cc_start: 0.7282 (m) cc_final: 0.6657 (p) REVERT: A 209 GLN cc_start: 0.8606 (OUTLIER) cc_final: 0.8354 (mm110) REVERT: B 169 LEU cc_start: 0.7811 (mm) cc_final: 0.7558 (mp) REVERT: B 206 THR cc_start: 0.7306 (m) cc_final: 0.6692 (p) REVERT: B 209 GLN cc_start: 0.8599 (OUTLIER) cc_final: 0.8345 (mm110) outliers start: 7 outliers final: 4 residues processed: 62 average time/residue: 0.9257 time to fit residues: 59.7618 Evaluate side-chains 58 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 52 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 GLN Chi-restraints excluded: chain A residue 209 GLN Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain B residue 131 GLN Chi-restraints excluded: chain B residue 209 GLN Chi-restraints excluded: chain B residue 315 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 43 optimal weight: 0.0670 chunk 45 optimal weight: 0.9990 chunk 25 optimal weight: 0.9980 chunk 38 optimal weight: 0.7980 chunk 32 optimal weight: 0.9980 chunk 36 optimal weight: 0.6980 chunk 26 optimal weight: 0.3980 chunk 18 optimal weight: 0.9990 chunk 35 optimal weight: 0.2980 chunk 37 optimal weight: 0.1980 chunk 47 optimal weight: 0.8980 overall best weight: 0.3318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 209 GLN A 340 ASN B 209 GLN B 340 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.161881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.131989 restraints weight = 12647.332| |-----------------------------------------------------------------------------| r_work (start): 0.3701 rms_B_bonded: 1.80 r_work: 0.3603 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3493 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7406 moved from start: 0.2529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4312 Z= 0.129 Angle : 0.478 6.768 5884 Z= 0.243 Chirality : 0.036 0.121 680 Planarity : 0.004 0.037 686 Dihedral : 4.980 35.304 676 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.35 % Allowed : 14.80 % Favored : 83.86 % 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: 3.39 (0.37), residues: 488 helix: 2.71 (0.24), residues: 422 sheet: None (None), residues: 0 loop : -1.13 (0.74), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 165 TYR 0.014 0.002 TYR A 236 PHE 0.012 0.001 PHE B 350 TRP 0.013 0.001 TRP A 219 HIS 0.005 0.001 HIS B 92 Details of bonding type rmsd covalent geometry : bond 0.00287 ( 4312) covalent geometry : angle 0.47797 ( 5884) hydrogen bonds : bond 0.03503 ( 336) hydrogen bonds : angle 4.20647 ( 996) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 54 time to evaluate : 0.260 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 206 THR cc_start: 0.7265 (m) cc_final: 0.6624 (p) REVERT: B 206 THR cc_start: 0.7313 (m) cc_final: 0.6680 (p) outliers start: 6 outliers final: 4 residues processed: 60 average time/residue: 0.8292 time to fit residues: 52.1285 Evaluate side-chains 57 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 53 time to evaluate : 0.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 GLN Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain B residue 131 GLN Chi-restraints excluded: chain B residue 315 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 37 optimal weight: 0.9980 chunk 5 optimal weight: 0.0470 chunk 27 optimal weight: 0.9990 chunk 12 optimal weight: 0.9980 chunk 35 optimal weight: 0.9980 chunk 13 optimal weight: 0.9990 chunk 8 optimal weight: 0.0970 chunk 23 optimal weight: 0.8980 chunk 16 optimal weight: 0.2980 chunk 30 optimal weight: 0.5980 chunk 28 optimal weight: 0.6980 overall best weight: 0.3476 ------------------------------------------------------------------------------- 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 = 0.4021 r_free = 0.4021 target = 0.162206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.132473 restraints weight = 12733.381| |-----------------------------------------------------------------------------| r_work (start): 0.3704 rms_B_bonded: 1.79 r_work: 0.3607 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3496 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7402 moved from start: 0.2412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4312 Z= 0.126 Angle : 0.473 7.333 5884 Z= 0.240 Chirality : 0.036 0.121 680 Planarity : 0.004 0.037 686 Dihedral : 4.959 35.140 676 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.12 % Allowed : 14.57 % Favored : 84.30 % 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: 3.47 (0.37), residues: 488 helix: 2.76 (0.24), residues: 422 sheet: None (None), residues: 0 loop : -1.08 (0.75), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 165 TYR 0.014 0.002 TYR A 236 PHE 0.004 0.001 PHE B 308 TRP 0.016 0.001 TRP B 219 HIS 0.005 0.001 HIS B 92 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 4312) covalent geometry : angle 0.47270 ( 5884) hydrogen bonds : bond 0.03456 ( 336) hydrogen bonds : angle 4.16212 ( 996) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 52 time to evaluate : 0.185 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 206 THR cc_start: 0.7235 (m) cc_final: 0.6603 (p) REVERT: B 169 LEU cc_start: 0.7810 (mm) cc_final: 0.7577 (mp) REVERT: B 206 THR cc_start: 0.7272 (m) cc_final: 0.6648 (p) outliers start: 5 outliers final: 4 residues processed: 57 average time/residue: 0.8881 time to fit residues: 53.0274 Evaluate side-chains 56 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 52 time to evaluate : 0.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 GLN Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain B residue 131 GLN Chi-restraints excluded: chain B residue 315 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 37 optimal weight: 0.9980 chunk 29 optimal weight: 0.9980 chunk 31 optimal weight: 0.6980 chunk 8 optimal weight: 0.8980 chunk 12 optimal weight: 0.4980 chunk 32 optimal weight: 0.8980 chunk 10 optimal weight: 0.0980 chunk 28 optimal weight: 0.9990 chunk 0 optimal weight: 0.9990 chunk 48 optimal weight: 0.0980 chunk 33 optimal weight: 0.0980 overall best weight: 0.2980 ------------------------------------------------------------------------------- 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 = 0.4022 r_free = 0.4022 target = 0.162436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.132669 restraints weight = 12727.671| |-----------------------------------------------------------------------------| r_work (start): 0.3711 rms_B_bonded: 1.80 r_work: 0.3616 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3505 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7386 moved from start: 0.2557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4312 Z= 0.117 Angle : 0.476 7.524 5884 Z= 0.239 Chirality : 0.036 0.120 680 Planarity : 0.004 0.036 686 Dihedral : 4.908 34.685 676 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 1.12 % Allowed : 15.70 % Favored : 83.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.59 (0.37), residues: 488 helix: 2.84 (0.24), residues: 422 sheet: None (None), residues: 0 loop : -1.04 (0.76), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 165 TYR 0.013 0.002 TYR A 236 PHE 0.015 0.001 PHE A 350 TRP 0.017 0.001 TRP B 219 HIS 0.005 0.001 HIS B 92 Details of bonding type rmsd covalent geometry : bond 0.00259 ( 4312) covalent geometry : angle 0.47558 ( 5884) hydrogen bonds : bond 0.03390 ( 336) hydrogen bonds : angle 4.09341 ( 996) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 51 time to evaluate : 0.182 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 206 THR cc_start: 0.7179 (m) cc_final: 0.6536 (p) REVERT: B 206 THR cc_start: 0.7215 (m) cc_final: 0.6589 (p) outliers start: 5 outliers final: 5 residues processed: 56 average time/residue: 0.8699 time to fit residues: 51.0016 Evaluate side-chains 56 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 51 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 GLN Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain B residue 131 GLN Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 315 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 8 optimal weight: 0.8980 chunk 37 optimal weight: 0.9980 chunk 44 optimal weight: 0.9980 chunk 32 optimal weight: 0.5980 chunk 38 optimal weight: 0.9980 chunk 33 optimal weight: 0.2980 chunk 23 optimal weight: 0.0030 chunk 9 optimal weight: 0.0870 chunk 35 optimal weight: 0.3980 chunk 13 optimal weight: 0.0010 chunk 28 optimal weight: 0.9980 overall best weight: 0.1574 ------------------------------------------------------------------------------- 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 = 0.4059 r_free = 0.4059 target = 0.165867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.135890 restraints weight = 12631.009| |-----------------------------------------------------------------------------| r_work (start): 0.3734 rms_B_bonded: 1.83 r_work: 0.3638 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3528 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7357 moved from start: 0.2415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 4312 Z= 0.102 Angle : 0.465 7.860 5884 Z= 0.235 Chirality : 0.035 0.119 680 Planarity : 0.004 0.036 686 Dihedral : 4.752 33.832 676 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 1.12 % Allowed : 15.47 % Favored : 83.41 % 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: 3.83 (0.38), residues: 488 helix: 3.01 (0.24), residues: 422 sheet: None (None), residues: 0 loop : -1.06 (0.75), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 165 TYR 0.011 0.001 TYR A 140 PHE 0.004 0.001 PHE B 207 TRP 0.017 0.001 TRP A 219 HIS 0.004 0.001 HIS A 92 Details of bonding type rmsd covalent geometry : bond 0.00218 ( 4312) covalent geometry : angle 0.46511 ( 5884) hydrogen bonds : bond 0.03278 ( 336) hydrogen bonds : angle 3.95240 ( 996) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2937.83 seconds wall clock time: 50 minutes 23.69 seconds (3023.69 seconds total)