Starting phenix.real_space_refine on Thu Jul 2 00:40:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bsn_44870/07_2026/9bsn_44870_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bsn_44870/07_2026/9bsn_44870.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9bsn_44870/07_2026/9bsn_44870_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bsn_44870/07_2026/9bsn_44870_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9bsn_44870/07_2026/9bsn_44870.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bsn_44870/07_2026/9bsn_44870.map" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.015 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 K 4 8.98 5 S 28 5.16 5 C 2920 2.51 5 N 678 2.21 5 O 712 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 4342 Number of models: 1 Model: "" Number of chains: 4 Chain: "U" Number of atoms: 2057 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2057 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 4, 'TRANS': 252} Chain breaks: 1 Chain: "A" Number of atoms: 2057 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2057 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 4, 'TRANS': 252} Chain breaks: 1 Chain: "U" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 112 Unusual residues: {'D10': 4, 'D12': 1, 'EIC': 1, 'OCT': 5} Classifications: {'undetermined': 11} Link IDs: {None: 10} Chain: "A" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 112 Ad-hoc single atom residues: {' K': 4} Unusual residues: {'D10': 4, 'D12': 1, 'EIC': 1, 'OCT': 5} Classifications: {'undetermined': 11} Link IDs: {None: 10} Chain breaks: 4 Time building chain proxies: 1.13, per 1000 atoms: 0.26 Number of scatterers: 4342 At special positions: 0 Unit cell: (69.66, 61.06, 95.46, 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) K 4 19.00 S 28 16.00 O 712 8.00 N 678 7.00 C 2920 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 156.8 milliseconds 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 952 Finding SS restraints... Secondary structure from input PDB file: 14 helices and 0 sheets defined 79.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.10 Creating SS restraints... Processing helix chain 'U' and resid 14 through 65 removed outlier: 5.782A pdb=" N ALA U 44 " --> pdb=" O ALA U 40 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N HIS U 45 " --> pdb=" O LEU U 41 " (cutoff:3.500A) Processing helix chain 'U' and resid 67 through 83 removed outlier: 3.527A pdb=" N LEU U 71 " --> pdb=" O SER U 67 " (cutoff:3.500A) Processing helix chain 'U' and resid 97 through 109 removed outlier: 3.530A pdb=" N SER U 109 " --> pdb=" O GLY U 105 " (cutoff:3.500A) Processing helix chain 'U' and resid 122 through 162 removed outlier: 3.537A pdb=" N PHE U 126 " --> pdb=" O GLY U 122 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N SER U 136 " --> pdb=" O LEU U 132 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N SER U 137 " --> pdb=" O VAL U 133 " (cutoff:3.500A) Processing helix chain 'U' and resid 193 through 215 removed outlier: 3.989A pdb=" N MET U 215 " --> pdb=" O CYS U 211 " (cutoff:3.500A) Processing helix chain 'U' and resid 223 through 236 Processing helix chain 'U' and resid 255 through 294 removed outlier: 3.725A pdb=" N PHE U 259 " --> pdb=" O GLY U 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 15 through 64 removed outlier: 5.745A pdb=" N ALA A 44 " --> pdb=" O ALA A 40 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N HIS A 45 " --> pdb=" O LEU A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 85 Processing helix chain 'A' and resid 96 through 109 removed outlier: 3.565A pdb=" N SER A 109 " --> pdb=" O GLY A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 162 removed outlier: 3.546A pdb=" N PHE A 126 " --> pdb=" O GLY A 122 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N SER A 136 " --> pdb=" O LEU A 132 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N SER A 137 " --> pdb=" O VAL A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 220 removed outlier: 3.607A pdb=" N MET A 215 " --> pdb=" O CYS A 211 " (cutoff:3.500A) Proline residue: A 218 - end of helix Processing helix chain 'A' and resid 223 through 236 Processing helix chain 'A' and resid 255 through 294 removed outlier: 3.808A pdb=" N PHE A 259 " --> pdb=" O GLY A 255 " (cutoff:3.500A) 330 hydrogen bonds defined for protein. 990 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.60 Time building geometry restraints manager: 0.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 702 1.33 - 1.45: 1219 1.45 - 1.57: 2459 1.57 - 1.69: 0 1.69 - 1.81: 40 Bond restraints: 4420 Sorted by residual: bond pdb=" N THR U 82 " pdb=" CA THR U 82 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.21e-02 6.83e+03 5.86e+00 bond pdb=" N LEU A 127 " pdb=" CA LEU A 127 " ideal model delta sigma weight residual 1.459 1.487 -0.028 1.19e-02 7.06e+03 5.49e+00 bond pdb=" N GLU A 46 " pdb=" CA GLU A 46 " ideal model delta sigma weight residual 1.459 1.487 -0.028 1.19e-02 7.06e+03 5.39e+00 bond pdb=" N LEU U 127 " pdb=" CA LEU U 127 " ideal model delta sigma weight residual 1.459 1.487 -0.028 1.21e-02 6.83e+03 5.34e+00 bond pdb=" N ASP A 242 " pdb=" CA ASP A 242 " ideal model delta sigma weight residual 1.459 1.486 -0.027 1.23e-02 6.61e+03 4.84e+00 ... (remaining 4415 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.33: 5592 1.33 - 2.66: 254 2.66 - 4.00: 29 4.00 - 5.33: 11 5.33 - 6.66: 4 Bond angle restraints: 5890 Sorted by residual: angle pdb=" C GLU A 252 " pdb=" CA GLU A 252 " pdb=" CB GLU A 252 " ideal model delta sigma weight residual 117.23 110.57 6.66 1.36e+00 5.41e-01 2.40e+01 angle pdb=" N ASP A 89 " pdb=" CA ASP A 89 " pdb=" C ASP A 89 " ideal model delta sigma weight residual 109.54 116.18 -6.64 1.37e+00 5.33e-01 2.35e+01 angle pdb=" N ASN A 90 " pdb=" CA ASN A 90 " pdb=" C ASN A 90 " ideal model delta sigma weight residual 111.28 115.45 -4.17 1.35e+00 5.49e-01 9.53e+00 angle pdb=" CA ASP A 89 " pdb=" C ASP A 89 " pdb=" O ASP A 89 " ideal model delta sigma weight residual 121.94 116.78 5.16 1.68e+00 3.54e-01 9.45e+00 angle pdb=" CA TYR A 251 " pdb=" C TYR A 251 " pdb=" O TYR A 251 " ideal model delta sigma weight residual 121.89 118.33 3.56 1.29e+00 6.01e-01 7.63e+00 ... (remaining 5885 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.98: 2170 15.98 - 31.95: 277 31.95 - 47.93: 93 47.93 - 63.90: 27 63.90 - 79.88: 1 Dihedral angle restraints: 2568 sinusoidal: 1080 harmonic: 1488 Sorted by residual: dihedral pdb=" CA ASP U 96 " pdb=" C ASP U 96 " pdb=" N PHE U 97 " pdb=" CA PHE U 97 " ideal model delta harmonic sigma weight residual 180.00 154.68 25.32 0 5.00e+00 4.00e-02 2.56e+01 dihedral pdb=" CA TRP A 95 " pdb=" C TRP A 95 " pdb=" N ASP A 96 " pdb=" CA ASP A 96 " ideal model delta harmonic sigma weight residual 180.00 159.68 20.32 0 5.00e+00 4.00e-02 1.65e+01 dihedral pdb=" CA LEU U 41 " pdb=" C LEU U 41 " pdb=" N GLU U 42 " pdb=" CA GLU U 42 " ideal model delta harmonic sigma weight residual 180.00 -163.40 -16.60 0 5.00e+00 4.00e-02 1.10e+01 ... (remaining 2565 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 498 0.037 - 0.074: 102 0.074 - 0.111: 28 0.111 - 0.147: 5 0.147 - 0.184: 1 Chirality restraints: 634 Sorted by residual: chirality pdb=" CA TYR A 251 " pdb=" N TYR A 251 " pdb=" C TYR A 251 " pdb=" CB TYR A 251 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 8.48e-01 chirality pdb=" CA THR A 217 " pdb=" N THR A 217 " pdb=" C THR A 217 " pdb=" CB THR A 217 " both_signs ideal model delta sigma weight residual False 2.53 2.40 0.12 2.00e-01 2.50e+01 3.88e-01 chirality pdb=" CA LEU A 127 " pdb=" N LEU A 127 " pdb=" C LEU A 127 " pdb=" CB LEU A 127 " both_signs ideal model delta sigma weight residual False 2.51 2.63 -0.12 2.00e-01 2.50e+01 3.40e-01 ... (remaining 631 not shown) Planarity restraints: 712 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA HIS A 250 " -0.009 2.00e-02 2.50e+03 1.83e-02 3.35e+00 pdb=" C HIS A 250 " 0.032 2.00e-02 2.50e+03 pdb=" O HIS A 250 " -0.012 2.00e-02 2.50e+03 pdb=" N TYR A 251 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR U 217 " -0.017 5.00e-02 4.00e+02 2.64e-02 1.12e+00 pdb=" N PRO U 218 " 0.046 5.00e-02 4.00e+02 pdb=" CA PRO U 218 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO U 218 " -0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 217 " 0.017 5.00e-02 4.00e+02 2.50e-02 1.00e+00 pdb=" N PRO A 218 " -0.043 5.00e-02 4.00e+02 pdb=" CA PRO A 218 " 0.012 5.00e-02 4.00e+02 pdb=" CD PRO A 218 " 0.014 5.00e-02 4.00e+02 ... (remaining 709 not shown) Histogram of nonbonded interaction distances: 2.36 - 2.92: 1746 2.92 - 3.47: 4785 3.47 - 4.03: 7050 4.03 - 4.58: 10754 4.58 - 5.14: 14844 Nonbonded interactions: 39179 Sorted by model distance: nonbonded pdb=" OH TYR U 216 " pdb=" OD1 ASN U 261 " model vdw 2.363 3.040 nonbonded pdb=" N ASP U 242 " pdb=" OD1 ASP U 242 " model vdw 2.368 3.120 nonbonded pdb=" O SER A 236 " pdb=" OG1 THR A 237 " model vdw 2.377 3.040 nonbonded pdb=" O SER U 109 " pdb=" OG1 THR U 110 " model vdw 2.396 3.040 nonbonded pdb=" N ASP U 96 " pdb=" OD1 ASP U 96 " model vdw 2.397 3.120 ... (remaining 39174 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 14 through 295 or resid 403 through 404 or resid 406 throu \ gh 408)) selection = (chain 'U' and (resid 14 through 295 or resid 403 through 404 or resid 406 throu \ gh 408)) } 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: 2.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 5.510 Find NCS groups from input model: 0.080 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:6.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8779 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 4420 Z= 0.215 Angle : 0.623 6.659 5890 Z= 0.367 Chirality : 0.035 0.184 634 Planarity : 0.003 0.026 712 Dihedral : 16.285 79.880 1616 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 2.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 0.92 % Allowed : 16.36 % Favored : 82.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.46 (0.38), residues: 506 helix: 4.12 (0.24), residues: 396 sheet: None (None), residues: 0 loop : -2.00 (0.52), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 68 TYR 0.010 0.001 TYR U 229 PHE 0.012 0.001 PHE U 232 TRP 0.012 0.001 TRP U 222 HIS 0.003 0.001 HIS U 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.22 ( 4420) covalent geometry : angle 0.62331 / 0.37 ( 5890) hydrogen bonds : bond 0.11460 / 7.39 ( 330) hydrogen bonds : angle 3.54514 / 2.72 ( 990) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 70 time to evaluate : 0.167 Fit side-chains revert: symmetry clash REVERT: A 251 TYR cc_start: 0.8406 (OUTLIER) cc_final: 0.7494 (t80) outliers start: 4 outliers final: 0 residues processed: 73 average time/residue: 0.7095 time to fit residues: 53.2472 Evaluate side-chains 54 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 53 time to evaluate : 0.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 24 optimal weight: 0.9980 chunk 48 optimal weight: 0.9990 chunk 26 optimal weight: 0.9990 chunk 2 optimal weight: 0.9990 chunk 16 optimal weight: 0.6980 chunk 32 optimal weight: 0.9990 chunk 31 optimal weight: 0.8980 chunk 25 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 22 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 90 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.096845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.074831 restraints weight = 7603.078| |-----------------------------------------------------------------------------| r_work (start): 0.2857 rms_B_bonded: 2.76 r_work: 0.2711 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.1678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 4420 Z= 0.149 Angle : 0.475 5.390 5890 Z= 0.268 Chirality : 0.033 0.117 634 Planarity : 0.003 0.024 712 Dihedral : 9.669 74.791 720 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 1.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 1.61 % Allowed : 17.74 % Favored : 80.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.89 (0.38), residues: 506 helix: 4.14 (0.24), residues: 402 sheet: None (None), residues: 0 loop : -0.91 (0.66), residues: 104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 68 TYR 0.009 0.001 TYR A 155 PHE 0.008 0.001 PHE U 259 TRP 0.009 0.001 TRP U 95 HIS 0.003 0.001 HIS A 64 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.15 ( 4420) covalent geometry : angle 0.47526 / 0.27 ( 5890) hydrogen bonds : bond 0.07535 / 4.98 ( 330) hydrogen bonds : angle 3.04246 / 2.30 ( 990) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 70 time to evaluate : 0.166 Fit side-chains revert: symmetry clash REVERT: U 67 SER cc_start: 0.8084 (OUTLIER) cc_final: 0.7507 (p) REVERT: U 251 TYR cc_start: 0.8310 (OUTLIER) cc_final: 0.7692 (t80) REVERT: A 51 GLN cc_start: 0.8718 (tm-30) cc_final: 0.8513 (tm-30) REVERT: A 70 GLU cc_start: 0.8596 (mp0) cc_final: 0.8049 (mp0) REVERT: A 147 GLU cc_start: 0.8240 (tm-30) cc_final: 0.8027 (tm-30) REVERT: A 251 TYR cc_start: 0.8375 (OUTLIER) cc_final: 0.7659 (t80) outliers start: 7 outliers final: 1 residues processed: 74 average time/residue: 0.7178 time to fit residues: 54.6179 Evaluate side-chains 62 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 58 time to evaluate : 0.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 67 SER Chi-restraints excluded: chain U residue 207 LEU Chi-restraints excluded: chain U residue 251 TYR Chi-restraints excluded: chain A residue 251 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 39 optimal weight: 4.9990 chunk 37 optimal weight: 0.5980 chunk 4 optimal weight: 0.6980 chunk 26 optimal weight: 0.8980 chunk 18 optimal weight: 0.8980 chunk 44 optimal weight: 2.9990 chunk 43 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 0 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3221 r_free = 0.3221 target = 0.097186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.075150 restraints weight = 7606.928| |-----------------------------------------------------------------------------| r_work (start): 0.2871 rms_B_bonded: 2.76 r_work: 0.2729 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.1913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 4420 Z= 0.142 Angle : 0.450 5.358 5890 Z= 0.257 Chirality : 0.033 0.113 634 Planarity : 0.002 0.024 712 Dihedral : 8.685 64.180 720 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 2.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 1.38 % Allowed : 17.28 % Favored : 81.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 5.05 (0.38), residues: 506 helix: 4.21 (0.24), residues: 404 sheet: None (None), residues: 0 loop : -0.78 (0.69), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 292 TYR 0.008 0.001 TYR U 216 PHE 0.008 0.001 PHE U 259 TRP 0.008 0.001 TRP U 95 HIS 0.003 0.001 HIS U 64 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.14 ( 4420) covalent geometry : angle 0.44972 / 0.26 ( 5890) hydrogen bonds : bond 0.07208 / 4.76 ( 330) hydrogen bonds : angle 2.93281 / 2.22 ( 990) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 58 time to evaluate : 0.165 Fit side-chains REVERT: U 190 TRP cc_start: 0.7914 (m-10) cc_final: 0.7616 (m-10) REVERT: U 251 TYR cc_start: 0.8410 (OUTLIER) cc_final: 0.7714 (t80) REVERT: A 51 GLN cc_start: 0.8787 (tm-30) cc_final: 0.8532 (tm-30) REVERT: A 55 GLU cc_start: 0.9044 (tp30) cc_final: 0.8744 (tp30) REVERT: A 70 GLU cc_start: 0.8648 (mp0) cc_final: 0.8376 (mp0) REVERT: A 190 TRP cc_start: 0.8150 (m-10) cc_final: 0.7935 (m-10) REVERT: A 251 TYR cc_start: 0.8434 (OUTLIER) cc_final: 0.7419 (t80) outliers start: 6 outliers final: 1 residues processed: 62 average time/residue: 0.6636 time to fit residues: 42.4392 Evaluate side-chains 58 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 55 time to evaluate : 0.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 207 LEU Chi-restraints excluded: chain U residue 251 TYR Chi-restraints excluded: chain A residue 251 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 14 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 28 optimal weight: 0.8980 chunk 16 optimal weight: 0.5980 chunk 18 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 11 optimal weight: 0.6980 chunk 32 optimal weight: 4.9990 chunk 25 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3236 r_free = 0.3236 target = 0.096677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.075058 restraints weight = 7542.218| |-----------------------------------------------------------------------------| r_work (start): 0.2859 rms_B_bonded: 2.70 r_work: 0.2724 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.2120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 4420 Z= 0.141 Angle : 0.458 5.387 5890 Z= 0.260 Chirality : 0.033 0.115 634 Planarity : 0.003 0.023 712 Dihedral : 8.247 55.865 720 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 2.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 0.92 % Allowed : 18.66 % Favored : 80.41 % 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: 5.05 (0.38), residues: 506 helix: 4.25 (0.24), residues: 404 sheet: None (None), residues: 0 loop : -0.95 (0.67), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 292 TYR 0.008 0.001 TYR U 216 PHE 0.008 0.001 PHE U 259 TRP 0.008 0.001 TRP U 95 HIS 0.003 0.000 HIS A 64 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.14 ( 4420) covalent geometry : angle 0.45850 / 0.26 ( 5890) hydrogen bonds : bond 0.07095 / 4.69 ( 330) hydrogen bonds : angle 2.91252 / 2.22 ( 990) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 51 time to evaluate : 0.191 Fit side-chains REVERT: U 190 TRP cc_start: 0.7897 (m-10) cc_final: 0.7570 (m-10) REVERT: U 251 TYR cc_start: 0.8453 (OUTLIER) cc_final: 0.7690 (t80) REVERT: A 51 GLN cc_start: 0.8806 (tm-30) cc_final: 0.8568 (tm-30) REVERT: A 55 GLU cc_start: 0.9059 (tp30) cc_final: 0.8745 (tp30) outliers start: 4 outliers final: 2 residues processed: 54 average time/residue: 0.5703 time to fit residues: 31.8520 Evaluate side-chains 51 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 48 time to evaluate : 0.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 207 LEU Chi-restraints excluded: chain U residue 251 TYR Chi-restraints excluded: chain A residue 251 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 21 optimal weight: 0.9980 chunk 5 optimal weight: 0.6980 chunk 10 optimal weight: 0.0170 chunk 28 optimal weight: 0.7980 chunk 20 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 39 optimal weight: 5.9990 chunk 34 optimal weight: 0.2980 chunk 27 optimal weight: 0.8980 chunk 29 optimal weight: 0.9990 chunk 46 optimal weight: 2.9990 overall best weight: 0.5418 ------------------------------------------------------------------------------- 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 = 0.3286 r_free = 0.3286 target = 0.100530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.078827 restraints weight = 7516.178| |-----------------------------------------------------------------------------| r_work (start): 0.2934 rms_B_bonded: 2.69 r_work: 0.2799 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.2316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 4420 Z= 0.126 Angle : 0.432 5.342 5890 Z= 0.245 Chirality : 0.032 0.112 634 Planarity : 0.002 0.022 712 Dihedral : 7.491 54.587 720 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 2.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 0.69 % Allowed : 19.82 % Favored : 79.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 5.12 (0.38), residues: 506 helix: 4.31 (0.24), residues: 404 sheet: None (None), residues: 0 loop : -1.00 (0.66), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG U 292 TYR 0.008 0.001 TYR U 30 PHE 0.008 0.001 PHE U 232 TRP 0.009 0.001 TRP U 95 HIS 0.003 0.000 HIS A 64 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.13 ( 4420) covalent geometry : angle 0.43189 / 0.25 ( 5890) hydrogen bonds : bond 0.06291 / 4.14 ( 330) hydrogen bonds : angle 2.75283 / 2.10 ( 990) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 56 time to evaluate : 0.160 Fit side-chains REVERT: U 190 TRP cc_start: 0.7898 (m-10) cc_final: 0.7611 (m-10) REVERT: U 251 TYR cc_start: 0.8495 (OUTLIER) cc_final: 0.7700 (t80) REVERT: A 51 GLN cc_start: 0.8834 (tm-30) cc_final: 0.8597 (tm-30) REVERT: A 55 GLU cc_start: 0.9061 (tp30) cc_final: 0.8653 (tp30) outliers start: 3 outliers final: 2 residues processed: 59 average time/residue: 0.5957 time to fit residues: 36.4469 Evaluate side-chains 53 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 50 time to evaluate : 0.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 207 LEU Chi-restraints excluded: chain U residue 251 TYR Chi-restraints excluded: chain A residue 251 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 29 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 20 optimal weight: 0.7980 chunk 32 optimal weight: 0.8980 chunk 36 optimal weight: 0.6980 chunk 13 optimal weight: 0.9980 chunk 40 optimal weight: 0.6980 chunk 28 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 chunk 33 optimal weight: 0.6980 chunk 0 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3239 r_free = 0.3239 target = 0.097179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.075465 restraints weight = 7670.038| |-----------------------------------------------------------------------------| r_work (start): 0.2860 rms_B_bonded: 2.71 r_work: 0.2725 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.2249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4420 Z= 0.140 Angle : 0.454 5.378 5890 Z= 0.258 Chirality : 0.032 0.118 634 Planarity : 0.002 0.022 712 Dihedral : 7.604 56.028 720 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 2.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 0.69 % Allowed : 20.74 % Favored : 78.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 5.09 (0.38), residues: 506 helix: 4.30 (0.24), residues: 404 sheet: None (None), residues: 0 loop : -1.08 (0.65), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG U 292 TYR 0.010 0.001 TYR U 216 PHE 0.008 0.001 PHE U 259 TRP 0.008 0.001 TRP A 190 HIS 0.003 0.000 HIS A 64 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.14 ( 4420) covalent geometry : angle 0.45410 / 0.26 ( 5890) hydrogen bonds : bond 0.06950 / 4.60 ( 330) hydrogen bonds : angle 2.87215 / 2.20 ( 990) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 48 time to evaluate : 0.161 Fit side-chains REVERT: U 190 TRP cc_start: 0.7893 (m-10) cc_final: 0.7590 (m-10) REVERT: U 251 TYR cc_start: 0.8469 (OUTLIER) cc_final: 0.7690 (t80) REVERT: A 51 GLN cc_start: 0.8801 (tm-30) cc_final: 0.8541 (tm-30) REVERT: A 190 TRP cc_start: 0.8073 (m-10) cc_final: 0.7848 (m-10) outliers start: 3 outliers final: 2 residues processed: 51 average time/residue: 0.5677 time to fit residues: 30.0617 Evaluate side-chains 50 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 47 time to evaluate : 0.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 207 LEU Chi-restraints excluded: chain U residue 251 TYR Chi-restraints excluded: chain A residue 251 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 31 optimal weight: 0.7980 chunk 6 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 chunk 13 optimal weight: 0.8980 chunk 42 optimal weight: 0.8980 chunk 19 optimal weight: 0.9990 chunk 39 optimal weight: 4.9990 chunk 12 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 32 optimal weight: 0.9980 chunk 2 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 = 0.3214 r_free = 0.3214 target = 0.095497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.073855 restraints weight = 7694.644| |-----------------------------------------------------------------------------| r_work (start): 0.2835 rms_B_bonded: 2.70 r_work: 0.2698 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.2175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4420 Z= 0.150 Angle : 0.469 5.373 5890 Z= 0.266 Chirality : 0.033 0.126 634 Planarity : 0.002 0.022 712 Dihedral : 7.539 49.942 720 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 2.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 0.69 % Allowed : 20.97 % Favored : 78.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 5.06 (0.38), residues: 506 helix: 4.31 (0.24), residues: 402 sheet: None (None), residues: 0 loop : -1.11 (0.64), residues: 104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG U 292 TYR 0.009 0.001 TYR U 216 PHE 0.008 0.001 PHE U 232 TRP 0.008 0.001 TRP A 190 HIS 0.003 0.000 HIS A 64 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.15 ( 4420) covalent geometry : angle 0.46930 / 0.27 ( 5890) hydrogen bonds : bond 0.07375 / 4.88 ( 330) hydrogen bonds : angle 2.95484 / 2.26 ( 990) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 49 time to evaluate : 0.152 Fit side-chains REVERT: U 190 TRP cc_start: 0.7892 (m-10) cc_final: 0.7615 (m-10) REVERT: U 251 TYR cc_start: 0.8510 (OUTLIER) cc_final: 0.7606 (t80) REVERT: A 51 GLN cc_start: 0.8857 (tm-30) cc_final: 0.8532 (tm-30) outliers start: 3 outliers final: 1 residues processed: 52 average time/residue: 0.5591 time to fit residues: 30.2144 Evaluate side-chains 49 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 47 time to evaluate : 0.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 207 LEU Chi-restraints excluded: chain U residue 251 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 27 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 9 optimal weight: 0.3980 chunk 21 optimal weight: 0.7980 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 = 0.3221 r_free = 0.3221 target = 0.096112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.074593 restraints weight = 7576.101| |-----------------------------------------------------------------------------| r_work (start): 0.2867 rms_B_bonded: 2.66 r_work: 0.2730 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.2320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4420 Z= 0.145 Angle : 0.471 6.030 5890 Z= 0.267 Chirality : 0.033 0.125 634 Planarity : 0.002 0.021 712 Dihedral : 7.009 40.062 718 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 2.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 0.92 % Allowed : 20.51 % Favored : 78.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 5.04 (0.38), residues: 506 helix: 4.29 (0.24), residues: 404 sheet: None (None), residues: 0 loop : -1.17 (0.64), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG U 292 TYR 0.015 0.001 TYR A 155 PHE 0.007 0.001 PHE U 232 TRP 0.010 0.001 TRP A 190 HIS 0.002 0.000 HIS A 64 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.14 ( 4420) covalent geometry : angle 0.47081 / 0.27 ( 5890) hydrogen bonds : bond 0.07132 / 4.71 ( 330) hydrogen bonds : angle 2.91003 / 2.23 ( 990) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 48 time to evaluate : 0.164 Fit side-chains REVERT: U 190 TRP cc_start: 0.7818 (m-10) cc_final: 0.7586 (m-10) REVERT: U 251 TYR cc_start: 0.8526 (OUTLIER) cc_final: 0.7604 (t80) REVERT: A 51 GLN cc_start: 0.8890 (tm-30) cc_final: 0.8560 (tm-30) outliers start: 4 outliers final: 2 residues processed: 51 average time/residue: 0.5613 time to fit residues: 29.6833 Evaluate side-chains 50 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 47 time to evaluate : 0.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 207 LEU Chi-restraints excluded: chain U residue 251 TYR Chi-restraints excluded: chain A residue 191 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 20 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 chunk 14 optimal weight: 5.9990 chunk 34 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 chunk 10 optimal weight: 0.6980 chunk 2 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 = 0.3205 r_free = 0.3205 target = 0.096439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.074839 restraints weight = 7655.548| |-----------------------------------------------------------------------------| r_work (start): 0.2858 rms_B_bonded: 2.73 r_work: 0.2714 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.2325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4420 Z= 0.148 Angle : 0.487 7.133 5890 Z= 0.274 Chirality : 0.033 0.140 634 Planarity : 0.002 0.021 712 Dihedral : 6.993 39.254 718 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 1.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 0.92 % Allowed : 20.74 % Favored : 78.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 5.01 (0.38), residues: 506 helix: 4.28 (0.24), residues: 404 sheet: None (None), residues: 0 loop : -1.26 (0.64), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG U 292 TYR 0.009 0.001 TYR U 216 PHE 0.008 0.001 PHE U 232 TRP 0.008 0.001 TRP U 95 HIS 0.003 0.000 HIS A 64 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.15 ( 4420) covalent geometry : angle 0.48652 / 0.27 ( 5890) hydrogen bonds : bond 0.07180 / 4.75 ( 330) hydrogen bonds : angle 2.92541 / 2.24 ( 990) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 48 time to evaluate : 0.257 Fit side-chains REVERT: U 190 TRP cc_start: 0.7790 (m-10) cc_final: 0.7578 (m-10) REVERT: U 251 TYR cc_start: 0.8514 (OUTLIER) cc_final: 0.7613 (t80) REVERT: A 51 GLN cc_start: 0.8860 (tm-30) cc_final: 0.8533 (tm-30) outliers start: 4 outliers final: 2 residues processed: 51 average time/residue: 0.6061 time to fit residues: 32.1516 Evaluate side-chains 51 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 48 time to evaluate : 0.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 207 LEU Chi-restraints excluded: chain U residue 251 TYR Chi-restraints excluded: chain A residue 191 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 17 optimal weight: 0.7980 chunk 26 optimal weight: 3.9990 chunk 48 optimal weight: 0.8980 chunk 43 optimal weight: 1.9990 chunk 46 optimal weight: 0.5980 chunk 13 optimal weight: 0.9980 chunk 24 optimal weight: 0.7980 chunk 22 optimal weight: 0.5980 chunk 20 optimal weight: 3.9990 chunk 9 optimal weight: 0.3980 chunk 23 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3239 r_free = 0.3239 target = 0.098546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.076735 restraints weight = 7530.333| |-----------------------------------------------------------------------------| r_work (start): 0.2895 rms_B_bonded: 2.73 r_work: 0.2755 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 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 : 0.003 0.040 4420 Z= 0.137 Angle : 0.483 8.366 5890 Z= 0.271 Chirality : 0.033 0.147 634 Planarity : 0.002 0.020 712 Dihedral : 6.578 37.110 718 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 2.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 0.92 % Allowed : 20.97 % Favored : 78.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 5.12 (0.38), residues: 506 helix: 4.34 (0.24), residues: 404 sheet: None (None), residues: 0 loop : -1.17 (0.65), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG U 83 TYR 0.015 0.001 TYR A 155 PHE 0.008 0.001 PHE A 232 TRP 0.009 0.001 TRP U 95 HIS 0.004 0.000 HIS A 64 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.14 ( 4420) covalent geometry : angle 0.48289 / 0.27 ( 5890) hydrogen bonds : bond 0.06568 / 4.33 ( 330) hydrogen bonds : angle 2.79838 / 2.14 ( 990) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 49 time to evaluate : 0.258 Fit side-chains REVERT: U 251 TYR cc_start: 0.8505 (OUTLIER) cc_final: 0.7678 (t80) REVERT: A 51 GLN cc_start: 0.8821 (tm-30) cc_final: 0.8510 (tm-30) outliers start: 4 outliers final: 2 residues processed: 51 average time/residue: 0.5540 time to fit residues: 29.2572 Evaluate side-chains 52 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 49 time to evaluate : 0.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 207 LEU Chi-restraints excluded: chain U residue 251 TYR Chi-restraints excluded: chain A residue 156 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 32 optimal weight: 4.9990 chunk 8 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 23 optimal weight: 0.5980 chunk 33 optimal weight: 0.5980 chunk 45 optimal weight: 0.6980 chunk 2 optimal weight: 0.9990 chunk 27 optimal weight: 0.7980 chunk 38 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3229 r_free = 0.3229 target = 0.097996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.076040 restraints weight = 7631.864| |-----------------------------------------------------------------------------| r_work (start): 0.2878 rms_B_bonded: 2.75 r_work: 0.2737 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.2477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4420 Z= 0.142 Angle : 0.492 8.823 5890 Z= 0.277 Chirality : 0.033 0.160 634 Planarity : 0.002 0.020 712 Dihedral : 6.672 36.278 718 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 2.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 0.46 % Allowed : 21.43 % Favored : 78.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 5.08 (0.38), residues: 506 helix: 4.33 (0.23), residues: 404 sheet: None (None), residues: 0 loop : -1.26 (0.64), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG U 83 TYR 0.013 0.001 TYR A 155 PHE 0.007 0.001 PHE U 232 TRP 0.008 0.001 TRP U 95 HIS 0.003 0.000 HIS A 64 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.14 ( 4420) covalent geometry : angle 0.49227 / 0.28 ( 5890) hydrogen bonds : bond 0.06795 / 4.49 ( 330) hydrogen bonds : angle 2.84376 / 2.18 ( 990) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1403.08 seconds wall clock time: 24 minutes 42.05 seconds (1482.05 seconds total)