Starting phenix.real_space_refine on Thu Sep 10 22:56:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9u48_63834/09_2026/9u48_63834.cif Found real_map, /net/cci-nas-00/data/ceres_data/9u48_63834/09_2026/9u48_63834.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.99 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9u48_63834/09_2026/9u48_63834.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9u48_63834/09_2026/9u48_63834.map" model { file = "/net/cci-nas-00/data/ceres_data/9u48_63834/09_2026/9u48_63834.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9u48_63834/09_2026/9u48_63834.cif" } resolution = 2.99 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= 0.016 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1301 atoms to isotropic. 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 P 49 5.49 5 S 21 5.16 5 C 2206 2.51 5 N 666 2.21 5 O 848 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 3790 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2712 Classifications: {'peptide': 335} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 320} Chain breaks: 1 Chain: "B" Number of atoms: 1051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 1051 Classifications: {'RNA': 49} Modifications used: {'rna2p_pur': 8, 'rna2p_pyr': 2, 'rna3p_pur': 21, 'rna3p_pyr': 18} Link IDs: {'rna2p': 10, 'rna3p': 38} Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Classifications: {'peptide': 1} Residues with excluded nonbonded symmetry interactions: 3 residue: pdb=" P C B 36 " occ=0.50 ... (18 atoms not shown) pdb=" C6 C B 36 " occ=0.50 residue: pdb=" P U B 82 " occ=0.50 ... (18 atoms not shown) pdb=" C6 U B 82 " occ=0.50 residue: pdb=" P G B 83 " occ=0.50 ... (21 atoms not shown) pdb=" C4 G B 83 " occ=0.50 Time building chain proxies: 1.06, per 1000 atoms: 0.28 Number of scatterers: 3790 At special positions: 0 Unit cell: (59.76, 69.72, 90.47, 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 21 16.00 P 49 15.00 O 848 8.00 N 666 7.00 C 2206 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: 0.26 Conformation dependent library (CDL) restraints added in 97.2 milliseconds 662 Ramachandran restraints generated. 331 Oldfield, 0 Emsley, 331 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 638 Finding SS restraints... Secondary structure from input PDB file: 11 helices and 0 sheets defined 37.3% alpha, 0.0% beta 13 base pairs and 24 stacking pairs defined. Time for finding SS restraints: 0.45 Creating SS restraints... Processing helix chain 'A' and resid 65 through 79 Processing helix chain 'A' and resid 102 through 111 removed outlier: 3.697A pdb=" N MET A 110 " --> pdb=" O LEU A 106 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N TYR A 111 " --> pdb=" O GLY A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 135 Processing helix chain 'A' and resid 175 through 181 Processing helix chain 'A' and resid 202 through 215 removed outlier: 3.769A pdb=" N LYS A 215 " --> pdb=" O LEU A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 243 Proline residue: A 234 - end of helix Processing helix chain 'A' and resid 274 through 277 No H-bonds generated for 'chain 'A' and resid 274 through 277' Processing helix chain 'A' and resid 285 through 287 No H-bonds generated for 'chain 'A' and resid 285 through 287' Processing helix chain 'A' and resid 300 through 317 removed outlier: 6.744A pdb=" N ASP A 307 " --> pdb=" O CYS A 303 " (cutoff:3.500A) removed outlier: 5.638A pdb=" N ASP A 308 " --> pdb=" O ALA A 304 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ASN A 317 " --> pdb=" O PHE A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 346 Processing helix chain 'A' and resid 379 through 397 removed outlier: 3.617A pdb=" N ASN A 396 " --> pdb=" O ALA A 392 " (cutoff:3.500A) 72 hydrogen bonds defined for protein. 216 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 32 hydrogen bonds 52 hydrogen bond angles 0 basepair planarities 13 basepair parallelities 24 stacking parallelities Total time for adding SS restraints: 0.63 Time building geometry restraints manager: 0.38 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: 1019 1.34 - 1.46: 1028 1.46 - 1.57: 1801 1.57 - 1.69: 97 1.69 - 1.81: 32 Bond restraints: 3977 Sorted by residual: bond pdb=" C TYR A 70 " pdb=" N ILE A 71 " ideal model delta sigma weight residual 1.334 1.267 0.068 1.26e-02 6.30e+03 2.88e+01 bond pdb=" O3' G B 43 " pdb=" P A B 44 " ideal model delta sigma weight residual 1.607 1.651 -0.044 1.20e-02 6.94e+03 1.33e+01 bond pdb=" O3' A B 35 " pdb=" P C B 36 " ideal model delta sigma weight residual 1.607 1.651 -0.044 1.20e-02 6.94e+03 1.32e+01 bond pdb=" O3' G B 40 " pdb=" P A B 41 " ideal model delta sigma weight residual 1.607 1.639 -0.032 1.20e-02 6.94e+03 6.91e+00 bond pdb=" N3 C B 55 " pdb=" C4 C B 55 " ideal model delta sigma weight residual 1.335 1.317 0.018 7.00e-03 2.04e+04 6.34e+00 ... (remaining 3972 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.77: 5292 1.77 - 3.54: 286 3.54 - 5.32: 21 5.32 - 7.09: 8 7.09 - 8.86: 2 Bond angle restraints: 5609 Sorted by residual: angle pdb=" O5' G B 65 " pdb=" C5' G B 65 " pdb=" C4' G B 65 " ideal model delta sigma weight residual 109.40 113.27 -3.87 8.00e-01 1.56e+00 2.35e+01 angle pdb=" C3' A B 35 " pdb=" O3' A B 35 " pdb=" P C B 36 " ideal model delta sigma weight residual 119.70 125.33 -5.63 1.20e+00 6.94e-01 2.20e+01 angle pdb=" O5' U B 58 " pdb=" C5' U B 58 " pdb=" C4' U B 58 " ideal model delta sigma weight residual 109.40 112.88 -3.48 8.00e-01 1.56e+00 1.90e+01 angle pdb=" O3' G B 43 " pdb=" C3' G B 43 " pdb=" C2' G B 43 " ideal model delta sigma weight residual 113.70 107.14 6.56 1.60e+00 3.91e-01 1.68e+01 angle pdb=" C1' G B 75 " pdb=" N9 G B 75 " pdb=" C4 G B 75 " ideal model delta sigma weight residual 126.50 131.76 -5.26 1.30e+00 5.92e-01 1.64e+01 ... (remaining 5604 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.44: 2282 33.44 - 66.87: 164 66.87 - 100.31: 24 100.31 - 133.75: 1 133.75 - 167.18: 1 Dihedral angle restraints: 2472 sinusoidal: 1488 harmonic: 984 Sorted by residual: dihedral pdb=" C5' A B 35 " pdb=" C4' A B 35 " pdb=" C3' A B 35 " pdb=" O3' A B 35 " ideal model delta sinusoidal sigma weight residual 147.00 96.14 50.86 1 8.00e+00 1.56e-02 5.53e+01 dihedral pdb=" O4' A B 35 " pdb=" C4' A B 35 " pdb=" C3' A B 35 " pdb=" C2' A B 35 " ideal model delta sinusoidal sigma weight residual 24.00 -10.65 34.65 1 8.00e+00 1.56e-02 2.66e+01 dihedral pdb=" C3' A B 35 " pdb=" C4' A B 35 " pdb=" O4' A B 35 " pdb=" C1' A B 35 " ideal model delta sinusoidal sigma weight residual -2.00 27.76 -29.76 1 8.00e+00 1.56e-02 1.98e+01 ... (remaining 2469 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.106: 587 0.106 - 0.213: 64 0.213 - 0.319: 0 0.319 - 0.425: 0 0.425 - 0.531: 1 Chirality restraints: 652 Sorted by residual: chirality pdb=" C3' A B 35 " pdb=" C4' A B 35 " pdb=" O3' A B 35 " pdb=" C2' A B 35 " both_signs ideal model delta sigma weight residual False -2.74 -2.21 -0.53 2.00e-01 2.50e+01 7.06e+00 chirality pdb=" CA SAM A 401 " pdb=" N SAM A 401 " pdb=" C SAM A 401 " pdb=" CB SAM A 401 " both_signs ideal model delta sigma weight residual False 2.45 2.64 -0.19 2.00e-01 2.50e+01 9.28e-01 chirality pdb=" CA PRO A 300 " pdb=" N PRO A 300 " pdb=" C PRO A 300 " pdb=" CB PRO A 300 " both_signs ideal model delta sigma weight residual False 2.72 2.54 0.17 2.00e-01 2.50e+01 7.65e-01 ... (remaining 649 not shown) Planarity restraints: 527 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR A 70 " -0.011 2.00e-02 2.50e+03 2.15e-02 4.61e+00 pdb=" C TYR A 70 " 0.037 2.00e-02 2.50e+03 pdb=" O TYR A 70 " -0.014 2.00e-02 2.50e+03 pdb=" N ILE A 71 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G B 43 " 0.026 2.00e-02 2.50e+03 1.21e-02 4.37e+00 pdb=" N9 G B 43 " -0.029 2.00e-02 2.50e+03 pdb=" C8 G B 43 " -0.000 2.00e-02 2.50e+03 pdb=" N7 G B 43 " 0.002 2.00e-02 2.50e+03 pdb=" C5 G B 43 " -0.003 2.00e-02 2.50e+03 pdb=" C6 G B 43 " -0.006 2.00e-02 2.50e+03 pdb=" O6 G B 43 " 0.014 2.00e-02 2.50e+03 pdb=" N1 G B 43 " -0.001 2.00e-02 2.50e+03 pdb=" C2 G B 43 " -0.001 2.00e-02 2.50e+03 pdb=" N2 G B 43 " 0.001 2.00e-02 2.50e+03 pdb=" N3 G B 43 " -0.001 2.00e-02 2.50e+03 pdb=" C4 G B 43 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A 233 " 0.034 5.00e-02 4.00e+02 5.20e-02 4.33e+00 pdb=" N PRO A 234 " -0.090 5.00e-02 4.00e+02 pdb=" CA PRO A 234 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 234 " 0.029 5.00e-02 4.00e+02 ... (remaining 524 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 483 2.74 - 3.28: 3642 3.28 - 3.82: 6851 3.82 - 4.36: 8037 4.36 - 4.90: 12493 Nonbonded interactions: 31506 Sorted by model distance: nonbonded pdb=" O LEU A 211 " pdb=" NZ LYS A 215 " model vdw 2.204 3.120 nonbonded pdb=" OH TYR A 172 " pdb=" O2' C B 36 " model vdw 2.238 3.040 nonbonded pdb=" NE ARG A 89 " pdb=" OD2 ASP A 114 " model vdw 2.259 3.120 nonbonded pdb=" O ARG A 217 " pdb=" OH TYR A 223 " model vdw 2.271 3.040 nonbonded pdb=" NZ LYS A 257 " pdb=" OP2 A B 39 " model vdw 2.295 3.120 ... (remaining 31501 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.50 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.250 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: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.650 Find NCS groups from input model: 0.010 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:7.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6821 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 : 0.006 0.068 3977 Z= 0.386 Angle : 0.832 8.861 5609 Z= 0.606 Chirality : 0.060 0.531 652 Planarity : 0.005 0.052 527 Dihedral : 20.562 167.183 1834 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 15.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % 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: -1.25 (0.48), residues: 331 helix: 0.56 (0.50), residues: 122 sheet: -1.43 (0.59), residues: 75 loop : -1.70 (0.53), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 260 TYR 0.017 0.002 TYR A 70 PHE 0.025 0.002 PHE A 125 TRP 0.014 0.002 TRP A 265 HIS 0.002 0.000 HIS A 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00602 / 0.39 ( 3977) covalent geometry : angle 0.83240 / 0.61 ( 5609) hydrogen bonds : bond 0.09284 / 6.43 ( 104) hydrogen bonds : angle 5.40376 / 3.99 ( 268) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 662 Ramachandran restraints generated. 331 Oldfield, 0 Emsley, 331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 662 Ramachandran restraints generated. 331 Oldfield, 0 Emsley, 331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 0.132 Fit side-chains revert: symmetry clash REVERT: A 263 ILE cc_start: 0.7659 (mt) cc_final: 0.7431 (mt) REVERT: A 297 THR cc_start: 0.7431 (t) cc_final: 0.7195 (m) outliers start: 0 outliers final: 0 residues processed: 61 average time/residue: 0.7155 time to fit residues: 44.6680 Evaluate side-chains 56 residues out of total 306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 24 optimal weight: 0.6980 chunk 26 optimal weight: 0.2980 chunk 2 optimal weight: 0.0470 chunk 16 optimal weight: 0.9990 chunk 32 optimal weight: 0.5980 chunk 31 optimal weight: 0.7980 chunk 25 optimal weight: 0.0980 chunk 19 optimal weight: 0.5980 chunk 30 optimal weight: 0.8980 chunk 22 optimal weight: 0.7980 chunk 13 optimal weight: 0.7980 overall best weight: 0.3278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.182158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.154760 restraints weight = 5184.414| |-----------------------------------------------------------------------------| r_work (start): 0.3987 rms_B_bonded: 2.05 r_work: 0.3864 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3864 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3867 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3867 r_free = 0.3867 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3868 r_free = 0.3868 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (15 function evaluations) r_final: 0.3868 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7100 moved from start: 0.1093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 3977 Z= 0.157 Angle : 0.605 9.070 5609 Z= 0.327 Chirality : 0.044 0.377 652 Planarity : 0.005 0.047 527 Dihedral : 22.035 140.303 1139 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 12.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 0.98 % Allowed : 11.44 % Favored : 87.58 % 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: -1.15 (0.48), residues: 331 helix: 0.69 (0.50), residues: 126 sheet: -1.64 (0.57), residues: 77 loop : -1.56 (0.57), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG A 72 TYR 0.015 0.002 TYR A 111 PHE 0.019 0.002 PHE A 178 TRP 0.010 0.002 TRP A 265 HIS 0.001 0.000 HIS A 290 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.16 ( 3977) covalent geometry : angle 0.60496 / 0.33 ( 5609) hydrogen bonds : bond 0.06163 / 4.14 ( 104) hydrogen bonds : angle 4.37224 / 3.08 ( 268) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 662 Ramachandran restraints generated. 331 Oldfield, 0 Emsley, 331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 662 Ramachandran restraints generated. 331 Oldfield, 0 Emsley, 331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 60 time to evaluate : 0.120 Fit side-chains REVERT: A 239 LYS cc_start: 0.7600 (mttm) cc_final: 0.7315 (mtpt) REVERT: A 263 ILE cc_start: 0.7803 (mt) cc_final: 0.7586 (mt) REVERT: A 270 MET cc_start: 0.7554 (mmp) cc_final: 0.7211 (mpp) outliers start: 3 outliers final: 3 residues processed: 60 average time/residue: 0.6684 time to fit residues: 41.2373 Evaluate side-chains 61 residues out of total 306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 58 time to evaluate : 0.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 91 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 16 optimal weight: 0.9990 chunk 19 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 chunk 9 optimal weight: 0.9990 chunk 28 optimal weight: 0.4980 chunk 1 optimal weight: 0.6980 chunk 24 optimal weight: 0.6980 chunk 3 optimal weight: 0.0170 chunk 18 optimal weight: 0.7980 chunk 32 optimal weight: 0.6980 overall best weight: 0.5218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.181196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.154542 restraints weight = 5085.915| |-----------------------------------------------------------------------------| r_work (start): 0.3986 rms_B_bonded: 1.98 r_work: 0.3865 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.3865 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3871 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3871 r_free = 0.3871 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3871 r_free = 0.3871 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.3871 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7106 moved from start: 0.1443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 3977 Z= 0.190 Angle : 0.594 7.097 5609 Z= 0.315 Chirality : 0.042 0.181 652 Planarity : 0.005 0.046 527 Dihedral : 21.534 116.531 1139 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 1.31 % Allowed : 15.03 % Favored : 83.66 % 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: -1.12 (0.48), residues: 331 helix: 0.65 (0.49), residues: 125 sheet: -1.49 (0.58), residues: 77 loop : -1.55 (0.57), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG A 391 TYR 0.009 0.002 TYR A 248 PHE 0.021 0.002 PHE A 125 TRP 0.010 0.002 TRP A 265 HIS 0.001 0.000 HIS A 273 Details of bonding type rmsd/Z covalent geometry : bond 0.00436 / 0.19 ( 3977) covalent geometry : angle 0.59427 / 0.31 ( 5609) hydrogen bonds : bond 0.06105 / 4.30 ( 104) hydrogen bonds : angle 4.27897 / 2.95 ( 268) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 662 Ramachandran restraints generated. 331 Oldfield, 0 Emsley, 331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 662 Ramachandran restraints generated. 331 Oldfield, 0 Emsley, 331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 56 time to evaluate : 0.115 Fit side-chains revert: symmetry clash REVERT: A 138 GLU cc_start: 0.6944 (mm-30) cc_final: 0.6269 (mm-30) REVERT: A 263 ILE cc_start: 0.7810 (mt) cc_final: 0.7581 (mt) REVERT: A 270 MET cc_start: 0.7556 (mmp) cc_final: 0.7205 (mpp) REVERT: A 285 SER cc_start: 0.8600 (t) cc_final: 0.8233 (m) REVERT: A 286 LYS cc_start: 0.8003 (ttmm) cc_final: 0.7757 (ttpp) REVERT: A 323 LYS cc_start: 0.7509 (tptt) cc_final: 0.7216 (tptm) outliers start: 4 outliers final: 3 residues processed: 58 average time/residue: 0.6515 time to fit residues: 38.7610 Evaluate side-chains 61 residues out of total 306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 58 time to evaluate : 0.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 275 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 9 optimal weight: 0.3980 chunk 10 optimal weight: 0.1980 chunk 4 optimal weight: 0.3980 chunk 15 optimal weight: 0.6980 chunk 32 optimal weight: 0.9990 chunk 29 optimal weight: 0.8980 chunk 2 optimal weight: 0.7980 chunk 7 optimal weight: 0.6980 chunk 33 optimal weight: 10.0000 chunk 22 optimal weight: 0.9990 chunk 21 optimal weight: 0.8980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.182051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.154458 restraints weight = 5220.117| |-----------------------------------------------------------------------------| r_work (start): 0.3984 rms_B_bonded: 2.09 r_work: 0.3861 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3861 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3858 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3858 r_free = 0.3858 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3858 r_free = 0.3858 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3858 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7117 moved from start: 0.1804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 3977 Z= 0.171 Angle : 0.572 6.498 5609 Z= 0.303 Chirality : 0.040 0.145 652 Planarity : 0.005 0.046 527 Dihedral : 21.262 104.590 1139 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 12.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 3.59 % Allowed : 17.32 % Favored : 79.08 % 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: -1.07 (0.48), residues: 331 helix: 0.62 (0.48), residues: 126 sheet: -1.38 (0.57), residues: 77 loop : -1.53 (0.58), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 391 TYR 0.008 0.001 TYR A 248 PHE 0.022 0.002 PHE A 178 TRP 0.009 0.002 TRP A 265 HIS 0.001 0.000 HIS A 273 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.17 ( 3977) covalent geometry : angle 0.57244 / 0.30 ( 5609) hydrogen bonds : bond 0.05978 / 4.34 ( 104) hydrogen bonds : angle 4.14749 / 2.87 ( 268) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 662 Ramachandran restraints generated. 331 Oldfield, 0 Emsley, 331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 662 Ramachandran restraints generated. 331 Oldfield, 0 Emsley, 331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 59 time to evaluate : 0.087 Fit side-chains REVERT: A 106 LEU cc_start: 0.8282 (mp) cc_final: 0.8071 (mm) REVERT: A 138 GLU cc_start: 0.6913 (mm-30) cc_final: 0.6096 (mm-30) REVERT: A 239 LYS cc_start: 0.7717 (OUTLIER) cc_final: 0.7381 (mtpt) REVERT: A 263 ILE cc_start: 0.7827 (mt) cc_final: 0.7591 (mt) REVERT: A 270 MET cc_start: 0.7572 (mmp) cc_final: 0.7210 (mpp) REVERT: A 285 SER cc_start: 0.8590 (t) cc_final: 0.8228 (m) REVERT: A 286 LYS cc_start: 0.8064 (ttmm) cc_final: 0.7796 (ttpp) REVERT: A 323 LYS cc_start: 0.7538 (tptt) cc_final: 0.7108 (tmtt) outliers start: 11 outliers final: 6 residues processed: 63 average time/residue: 0.6158 time to fit residues: 39.8154 Evaluate side-chains 66 residues out of total 306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 59 time to evaluate : 0.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 239 LYS Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 332 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 7 optimal weight: 0.4980 chunk 27 optimal weight: 0.5980 chunk 6 optimal weight: 0.3980 chunk 19 optimal weight: 0.8980 chunk 28 optimal weight: 0.0870 chunk 16 optimal weight: 0.1980 chunk 10 optimal weight: 0.0770 chunk 25 optimal weight: 0.5980 chunk 8 optimal weight: 0.9990 chunk 36 optimal weight: 4.9990 chunk 26 optimal weight: 0.5980 overall best weight: 0.2516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.182951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.156151 restraints weight = 5095.876| |-----------------------------------------------------------------------------| r_work (start): 0.4009 rms_B_bonded: 2.03 r_work: 0.3886 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3886 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3888 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3888 r_free = 0.3888 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3887 r_free = 0.3887 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (11 function evaluations) r_final: 0.3887 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7077 moved from start: 0.1974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3977 Z= 0.124 Angle : 0.545 7.592 5609 Z= 0.287 Chirality : 0.038 0.132 652 Planarity : 0.004 0.044 527 Dihedral : 21.104 102.917 1139 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.94 % Allowed : 18.95 % Favored : 78.10 % 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: -0.88 (0.48), residues: 331 helix: 0.84 (0.49), residues: 126 sheet: -1.31 (0.57), residues: 77 loop : -1.47 (0.57), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 146 TYR 0.007 0.001 TYR A 113 PHE 0.019 0.002 PHE A 206 TRP 0.008 0.001 TRP A 265 HIS 0.001 0.000 HIS A 195 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.12 ( 3977) covalent geometry : angle 0.54461 / 0.29 ( 5609) hydrogen bonds : bond 0.05437 / 3.94 ( 104) hydrogen bonds : angle 4.12578 / 2.83 ( 268) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 662 Ramachandran restraints generated. 331 Oldfield, 0 Emsley, 331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 662 Ramachandran restraints generated. 331 Oldfield, 0 Emsley, 331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 57 time to evaluate : 0.090 Fit side-chains REVERT: A 106 LEU cc_start: 0.8303 (mp) cc_final: 0.8080 (mm) REVERT: A 226 MET cc_start: 0.7505 (ttt) cc_final: 0.7092 (ttt) REVERT: A 239 LYS cc_start: 0.7686 (OUTLIER) cc_final: 0.7368 (mtpt) REVERT: A 263 ILE cc_start: 0.7765 (mt) cc_final: 0.7538 (mt) REVERT: A 270 MET cc_start: 0.7622 (mmp) cc_final: 0.7294 (mpp) REVERT: A 285 SER cc_start: 0.8587 (t) cc_final: 0.8233 (m) REVERT: A 286 LYS cc_start: 0.8034 (ttmm) cc_final: 0.7826 (ttpp) REVERT: A 312 LYS cc_start: 0.7221 (mmtt) cc_final: 0.6971 (mmtt) outliers start: 9 outliers final: 5 residues processed: 60 average time/residue: 0.6401 time to fit residues: 39.3829 Evaluate side-chains 62 residues out of total 306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 56 time to evaluate : 0.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 239 LYS Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 358 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 19 optimal weight: 0.3980 chunk 27 optimal weight: 0.3980 chunk 36 optimal weight: 4.9990 chunk 16 optimal weight: 0.5980 chunk 0 optimal weight: 7.9990 chunk 18 optimal weight: 0.5980 chunk 14 optimal weight: 0.5980 chunk 29 optimal weight: 0.4980 chunk 10 optimal weight: 0.8980 chunk 2 optimal weight: 0.9990 chunk 24 optimal weight: 0.8980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.182936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.155231 restraints weight = 5209.346| |-----------------------------------------------------------------------------| r_work (start): 0.3993 rms_B_bonded: 2.15 r_work: 0.3861 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3861 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3862 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3862 r_free = 0.3862 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3862 r_free = 0.3862 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.3862 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7108 moved from start: 0.2036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 3977 Z= 0.177 Angle : 0.568 6.843 5609 Z= 0.297 Chirality : 0.039 0.158 652 Planarity : 0.006 0.084 527 Dihedral : 21.019 103.253 1139 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 2.94 % Allowed : 18.30 % Favored : 78.76 % 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: -0.87 (0.48), residues: 331 helix: 0.83 (0.49), residues: 126 sheet: -1.27 (0.57), residues: 77 loop : -1.47 (0.57), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 391 TYR 0.009 0.001 TYR A 248 PHE 0.020 0.002 PHE A 125 TRP 0.007 0.002 TRP A 265 HIS 0.001 0.000 HIS A 273 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.18 ( 3977) covalent geometry : angle 0.56821 / 0.30 ( 5609) hydrogen bonds : bond 0.05647 / 4.30 ( 104) hydrogen bonds : angle 4.15762 / 2.85 ( 268) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 662 Ramachandran restraints generated. 331 Oldfield, 0 Emsley, 331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 662 Ramachandran restraints generated. 331 Oldfield, 0 Emsley, 331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 60 time to evaluate : 0.105 Fit side-chains revert: symmetry clash REVERT: A 106 LEU cc_start: 0.8219 (mp) cc_final: 0.7995 (mm) REVERT: A 111 TYR cc_start: 0.8257 (m-80) cc_final: 0.8038 (m-80) REVERT: A 137 MET cc_start: 0.8049 (mpt) cc_final: 0.7786 (mpt) REVERT: A 239 LYS cc_start: 0.7693 (OUTLIER) cc_final: 0.7314 (mtpt) REVERT: A 270 MET cc_start: 0.7672 (mmp) cc_final: 0.7320 (mpp) REVERT: A 285 SER cc_start: 0.8611 (t) cc_final: 0.8221 (m) REVERT: A 286 LYS cc_start: 0.8038 (ttmm) cc_final: 0.7820 (ttpp) REVERT: A 312 LYS cc_start: 0.7301 (mmtt) cc_final: 0.7041 (mmtt) REVERT: A 323 LYS cc_start: 0.7462 (tptt) cc_final: 0.7069 (tmtt) outliers start: 9 outliers final: 7 residues processed: 64 average time/residue: 0.6435 time to fit residues: 42.2652 Evaluate side-chains 67 residues out of total 306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 59 time to evaluate : 0.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 239 LYS Chi-restraints excluded: chain A residue 303 CYS Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 358 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 16 optimal weight: 0.6980 chunk 22 optimal weight: 0.0980 chunk 33 optimal weight: 10.0000 chunk 23 optimal weight: 0.9990 chunk 6 optimal weight: 0.6980 chunk 4 optimal weight: 0.0970 chunk 14 optimal weight: 0.6980 chunk 19 optimal weight: 0.9980 chunk 36 optimal weight: 4.9990 chunk 3 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 overall best weight: 0.4578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.183341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.156210 restraints weight = 5171.847| |-----------------------------------------------------------------------------| r_work (start): 0.4004 rms_B_bonded: 2.03 r_work: 0.3871 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3871 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3869 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3869 r_free = 0.3869 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3869 r_free = 0.3869 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (29 function evaluations) r_final: 0.3869 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7111 moved from start: 0.2181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 3977 Z= 0.163 Angle : 0.548 6.863 5609 Z= 0.286 Chirality : 0.039 0.137 652 Planarity : 0.004 0.046 527 Dihedral : 20.908 102.469 1139 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 3.27 % Allowed : 19.28 % Favored : 77.45 % 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: -0.85 (0.48), residues: 331 helix: 0.81 (0.49), residues: 126 sheet: -1.19 (0.58), residues: 77 loop : -1.47 (0.57), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 391 TYR 0.009 0.001 TYR A 248 PHE 0.018 0.002 PHE A 125 TRP 0.009 0.002 TRP A 265 HIS 0.001 0.000 HIS A 273 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.16 ( 3977) covalent geometry : angle 0.54815 / 0.29 ( 5609) hydrogen bonds : bond 0.05604 / 4.22 ( 104) hydrogen bonds : angle 4.12826 / 2.80 ( 268) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 662 Ramachandran restraints generated. 331 Oldfield, 0 Emsley, 331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 662 Ramachandran restraints generated. 331 Oldfield, 0 Emsley, 331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 59 time to evaluate : 0.119 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 137 MET cc_start: 0.7972 (mpt) cc_final: 0.7770 (mpt) REVERT: A 270 MET cc_start: 0.7588 (mmp) cc_final: 0.7253 (mpp) REVERT: A 285 SER cc_start: 0.8578 (t) cc_final: 0.8211 (m) REVERT: A 286 LYS cc_start: 0.8073 (ttmm) cc_final: 0.7864 (ttpp) REVERT: A 312 LYS cc_start: 0.7355 (mmtt) cc_final: 0.7079 (mmtt) REVERT: A 323 LYS cc_start: 0.7459 (tptt) cc_final: 0.7151 (tmtt) REVERT: A 391 ARG cc_start: 0.7619 (ttm-80) cc_final: 0.7295 (ttm170) outliers start: 10 outliers final: 10 residues processed: 62 average time/residue: 0.6072 time to fit residues: 38.6877 Evaluate side-chains 68 residues out of total 306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 58 time to evaluate : 0.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 239 LYS Chi-restraints excluded: chain A residue 303 CYS Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 358 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 34 optimal weight: 3.9990 chunk 9 optimal weight: 0.0370 chunk 10 optimal weight: 0.0980 chunk 29 optimal weight: 1.9990 chunk 14 optimal weight: 0.5980 chunk 36 optimal weight: 4.9990 chunk 3 optimal weight: 0.7980 chunk 26 optimal weight: 0.7980 chunk 7 optimal weight: 0.5980 chunk 0 optimal weight: 5.9990 chunk 12 optimal weight: 0.7980 overall best weight: 0.4258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.183980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.157008 restraints weight = 5137.780| |-----------------------------------------------------------------------------| r_work (start): 0.4014 rms_B_bonded: 1.97 r_work: 0.3883 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3883 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3884 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3884 r_free = 0.3884 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3885 r_free = 0.3885 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3885 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7097 moved from start: 0.2311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 3977 Z= 0.158 Angle : 0.540 7.548 5609 Z= 0.284 Chirality : 0.039 0.142 652 Planarity : 0.004 0.045 527 Dihedral : 20.832 101.867 1139 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 3.59 % Allowed : 19.93 % Favored : 76.47 % 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: -0.82 (0.48), residues: 331 helix: 0.86 (0.49), residues: 126 sheet: -1.20 (0.59), residues: 77 loop : -1.47 (0.56), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 391 TYR 0.009 0.001 TYR A 248 PHE 0.017 0.002 PHE A 125 TRP 0.010 0.002 TRP A 265 HIS 0.001 0.000 HIS A 195 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.16 ( 3977) covalent geometry : angle 0.53968 / 0.28 ( 5609) hydrogen bonds : bond 0.05521 / 4.18 ( 104) hydrogen bonds : angle 4.14954 / 2.84 ( 268) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 662 Ramachandran restraints generated. 331 Oldfield, 0 Emsley, 331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 662 Ramachandran restraints generated. 331 Oldfield, 0 Emsley, 331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 60 time to evaluate : 0.119 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 270 MET cc_start: 0.7552 (mmp) cc_final: 0.7218 (mpp) REVERT: A 285 SER cc_start: 0.8578 (t) cc_final: 0.8226 (m) REVERT: A 286 LYS cc_start: 0.8062 (ttmm) cc_final: 0.7854 (ttpp) REVERT: A 312 LYS cc_start: 0.7347 (mmtt) cc_final: 0.7121 (mmtt) REVERT: A 323 LYS cc_start: 0.7404 (tptt) cc_final: 0.7099 (tmtt) outliers start: 11 outliers final: 10 residues processed: 63 average time/residue: 0.6461 time to fit residues: 41.8216 Evaluate side-chains 71 residues out of total 306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 61 time to evaluate : 0.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 239 LYS Chi-restraints excluded: chain A residue 303 CYS Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 358 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 21 optimal weight: 0.0060 chunk 31 optimal weight: 0.8980 chunk 3 optimal weight: 0.9990 chunk 25 optimal weight: 0.5980 chunk 26 optimal weight: 0.5980 chunk 36 optimal weight: 4.9990 chunk 8 optimal weight: 0.9990 chunk 11 optimal weight: 0.0570 chunk 10 optimal weight: 0.5980 chunk 28 optimal weight: 2.9990 chunk 9 optimal weight: 0.0270 overall best weight: 0.2572 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4327 r_free = 0.4327 target = 0.185762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.158613 restraints weight = 5082.754| |-----------------------------------------------------------------------------| r_work (start): 0.4039 rms_B_bonded: 1.98 r_work: 0.3914 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3914 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3911 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3911 r_free = 0.3911 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3910 r_free = 0.3910 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3910 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7063 moved from start: 0.2476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3977 Z= 0.120 Angle : 0.556 8.833 5609 Z= 0.282 Chirality : 0.038 0.135 652 Planarity : 0.004 0.044 527 Dihedral : 20.785 100.591 1139 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 3.27 % Allowed : 20.59 % Favored : 76.14 % 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: -0.79 (0.48), residues: 331 helix: 0.85 (0.49), residues: 126 sheet: -1.21 (0.59), residues: 77 loop : -1.38 (0.56), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 146 TYR 0.008 0.001 TYR A 113 PHE 0.015 0.001 PHE A 178 TRP 0.010 0.001 TRP A 265 HIS 0.001 0.000 HIS A 195 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 ( 3977) covalent geometry : angle 0.55604 / 0.28 ( 5609) hydrogen bonds : bond 0.05202 / 3.89 ( 104) hydrogen bonds : angle 4.03234 / 2.74 ( 268) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 662 Ramachandran restraints generated. 331 Oldfield, 0 Emsley, 331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 662 Ramachandran restraints generated. 331 Oldfield, 0 Emsley, 331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 60 time to evaluate : 0.117 Fit side-chains revert: symmetry clash REVERT: A 82 SER cc_start: 0.6748 (OUTLIER) cc_final: 0.6497 (m) REVERT: A 239 LYS cc_start: 0.7666 (OUTLIER) cc_final: 0.7340 (mtpt) REVERT: A 270 MET cc_start: 0.7539 (mmp) cc_final: 0.7183 (mpp) REVERT: A 285 SER cc_start: 0.8546 (t) cc_final: 0.8207 (m) REVERT: A 286 LYS cc_start: 0.8039 (ttmm) cc_final: 0.7813 (ttpp) REVERT: A 312 LYS cc_start: 0.7305 (mmtt) cc_final: 0.7065 (mmtt) REVERT: A 323 LYS cc_start: 0.7393 (tptt) cc_final: 0.7157 (tmtt) REVERT: A 338 SER cc_start: 0.8314 (t) cc_final: 0.8103 (t) REVERT: A 391 ARG cc_start: 0.7558 (ttm-80) cc_final: 0.7258 (ttm170) outliers start: 10 outliers final: 7 residues processed: 62 average time/residue: 0.6551 time to fit residues: 41.7016 Evaluate side-chains 69 residues out of total 306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 60 time to evaluate : 0.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 239 LYS Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 358 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 13 optimal weight: 0.0670 chunk 0 optimal weight: 5.9990 chunk 16 optimal weight: 0.2980 chunk 12 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 chunk 22 optimal weight: 0.5980 chunk 6 optimal weight: 0.7980 chunk 24 optimal weight: 0.9980 chunk 29 optimal weight: 0.7980 chunk 19 optimal weight: 0.8980 chunk 14 optimal weight: 0.6980 overall best weight: 0.4718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 168 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.184129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.156527 restraints weight = 5130.575| |-----------------------------------------------------------------------------| r_work (start): 0.4012 rms_B_bonded: 2.03 r_work: 0.3881 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3881 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3883 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3883 r_free = 0.3883 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3883 r_free = 0.3883 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3883 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7103 moved from start: 0.2500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 3977 Z= 0.166 Angle : 0.575 9.704 5609 Z= 0.294 Chirality : 0.039 0.132 652 Planarity : 0.004 0.047 527 Dihedral : 20.718 101.633 1139 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 3.59 % Allowed : 19.61 % Favored : 76.80 % 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: -0.85 (0.48), residues: 331 helix: 0.83 (0.49), residues: 126 sheet: -1.29 (0.58), residues: 77 loop : -1.41 (0.55), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 271 TYR 0.010 0.001 TYR A 248 PHE 0.018 0.002 PHE A 125 TRP 0.007 0.002 TRP A 265 HIS 0.001 0.001 HIS A 273 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.17 ( 3977) covalent geometry : angle 0.57491 / 0.29 ( 5609) hydrogen bonds : bond 0.05529 / 4.32 ( 104) hydrogen bonds : angle 4.10654 / 2.78 ( 268) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 662 Ramachandran restraints generated. 331 Oldfield, 0 Emsley, 331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 662 Ramachandran restraints generated. 331 Oldfield, 0 Emsley, 331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 61 time to evaluate : 0.111 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 138 GLU cc_start: 0.7018 (mm-30) cc_final: 0.6099 (mm-30) REVERT: A 270 MET cc_start: 0.7566 (mmp) cc_final: 0.7239 (mpp) REVERT: A 285 SER cc_start: 0.8584 (t) cc_final: 0.8234 (m) REVERT: A 286 LYS cc_start: 0.8063 (ttmm) cc_final: 0.7848 (ttpp) REVERT: A 312 LYS cc_start: 0.7345 (mmtt) cc_final: 0.7093 (mmtt) REVERT: A 323 LYS cc_start: 0.7405 (tptt) cc_final: 0.7078 (tmtt) REVERT: A 391 ARG cc_start: 0.7564 (ttm-80) cc_final: 0.7260 (ttm170) outliers start: 11 outliers final: 8 residues processed: 63 average time/residue: 0.6386 time to fit residues: 41.2522 Evaluate side-chains 68 residues out of total 306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 60 time to evaluate : 0.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 239 LYS Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 358 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 24 optimal weight: 0.9980 chunk 12 optimal weight: 0.3980 chunk 5 optimal weight: 0.9990 chunk 8 optimal weight: 0.0270 chunk 34 optimal weight: 3.9990 chunk 30 optimal weight: 0.7980 chunk 31 optimal weight: 0.3980 chunk 29 optimal weight: 1.9990 chunk 14 optimal weight: 0.5980 chunk 25 optimal weight: 0.0040 chunk 0 optimal weight: 4.9990 overall best weight: 0.2850 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.186265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.158895 restraints weight = 5093.744| |-----------------------------------------------------------------------------| r_work (start): 0.4037 rms_B_bonded: 2.01 r_work: 0.3907 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3907 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3908 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3908 r_free = 0.3908 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3908 r_free = 0.3908 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3908 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7069 moved from start: 0.2624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3977 Z= 0.125 Angle : 0.557 10.244 5609 Z= 0.284 Chirality : 0.038 0.132 652 Planarity : 0.004 0.045 527 Dihedral : 20.669 100.251 1139 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 3.27 % Allowed : 19.93 % Favored : 76.80 % 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: -0.74 (0.48), residues: 331 helix: 0.87 (0.49), residues: 126 sheet: -1.22 (0.59), residues: 77 loop : -1.29 (0.56), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 146 TYR 0.006 0.001 TYR A 113 PHE 0.015 0.001 PHE A 178 TRP 0.010 0.001 TRP A 265 HIS 0.001 0.000 HIS A 195 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 ( 3977) covalent geometry : angle 0.55744 / 0.28 ( 5609) hydrogen bonds : bond 0.05204 / 3.90 ( 104) hydrogen bonds : angle 4.00601 / 2.70 ( 268) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1491.01 seconds wall clock time: 26 minutes 13.71 seconds (1573.71 seconds total)