Starting phenix.real_space_refine on Wed Sep 17 05:07:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bsn_44870/09_2025/9bsn_44870_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bsn_44870/09_2025/9bsn_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9bsn_44870/09_2025/9bsn_44870.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bsn_44870/09_2025/9bsn_44870.map" model { file = "/net/cci-nas-00/data/ceres_data/9bsn_44870/09_2025/9bsn_44870_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bsn_44870/09_2025/9bsn_44870_trim.cif" } 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/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, 116 Unusual residues: {' K': 4, 'D10': 4, 'D12': 1, 'EIC': 1, 'OCT': 5} Classifications: {'undetermined': 15} Link IDs: {None: 14} Time building chain proxies: 1.32, per 1000 atoms: 0.30 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: 0.45 Conformation dependent library (CDL) restraints added in 161.7 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.11 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: 0.59 Time building geometry restraints manager: 0.53 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: 1.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 6.190 Find NCS groups from input model: 0.070 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:6.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8640 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 aren 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 covalent geometry : bond 0.00367 ( 4420) covalent geometry : angle 0.62331 ( 5890) hydrogen bonds : bond 0.11460 ( 330) hydrogen bonds : angle 3.54514 ( 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 : 0.118 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: 0.7523 time to fit residues: 56.3990 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 : 0.169 ------------------------------------------------------------------------------- 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: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.096021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.074068 restraints weight = 7601.365| |-----------------------------------------------------------------------------| r_work (start): 0.2847 rms_B_bonded: 2.75 r_work: 0.2705 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.1622 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= 0.151 Angle : 0.475 5.413 5890 Z= 0.270 Chirality : 0.033 0.117 634 Planarity : 0.003 0.024 712 Dihedral : 9.641 74.277 720 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 1.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % 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 aren not related in a simple way. whole: 4.66 (0.38), residues: 506 helix: 4.13 (0.24), residues: 402 sheet: None (None), residues: 0 loop : -1.74 (0.56), residues: 104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG U 83 TYR 0.009 0.001 TYR A 155 PHE 0.009 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 covalent geometry : bond 0.00297 ( 4420) covalent geometry : angle 0.47521 ( 5890) hydrogen bonds : bond 0.07657 ( 330) hydrogen bonds : angle 3.05336 ( 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 : 0.147 Fit side-chains revert: symmetry clash REVERT: U 67 SER cc_start: 0.8119 (OUTLIER) cc_final: 0.7625 (p) REVERT: U 251 TYR cc_start: 0.8336 (OUTLIER) cc_final: 0.7745 (t80) REVERT: A 70 GLU cc_start: 0.8621 (mp0) cc_final: 0.8076 (mp0) REVERT: A 251 TYR cc_start: 0.8385 (OUTLIER) cc_final: 0.7651 (t80) outliers start: 7 outliers final: 1 residues processed: 74 average time/residue: 0.7376 time to fit residues: 56.0494 Evaluate side-chains 61 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 57 time to evaluate : 0.181 ------------------------------------------------------------------------------- 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: 0.9980 chunk 26 optimal weight: 0.9990 chunk 18 optimal weight: 0.9980 chunk 44 optimal weight: 0.7980 chunk 43 optimal weight: 0.7980 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 0 optimal weight: 1.9990 chunk 1 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.098170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.076440 restraints weight = 7575.555| |-----------------------------------------------------------------------------| r_work (start): 0.2876 rms_B_bonded: 2.73 r_work: 0.2734 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.1866 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= 0.141 Angle : 0.451 5.354 5890 Z= 0.258 Chirality : 0.033 0.114 634 Planarity : 0.002 0.024 712 Dihedral : 8.642 63.984 720 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 1.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 1.15 % Allowed : 17.51 % 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 aren not related in a simple way. whole: 4.79 (0.38), residues: 506 helix: 4.23 (0.24), residues: 402 sheet: None (None), residues: 0 loop : -1.70 (0.57), residues: 104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 292 TYR 0.007 0.001 TYR U 30 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 covalent geometry : bond 0.00273 ( 4420) covalent geometry : angle 0.45055 ( 5890) hydrogen bonds : bond 0.07143 ( 330) hydrogen bonds : angle 2.92046 ( 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 63 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 58 time to evaluate : 0.175 Fit side-chains REVERT: U 190 TRP cc_start: 0.7900 (m-10) cc_final: 0.7580 (m-10) REVERT: U 251 TYR cc_start: 0.8400 (OUTLIER) cc_final: 0.7704 (t80) REVERT: A 55 GLU cc_start: 0.9024 (tp30) cc_final: 0.8710 (tp30) REVERT: A 70 GLU cc_start: 0.8649 (mp0) cc_final: 0.8420 (mp0) REVERT: A 190 TRP cc_start: 0.8152 (m-10) cc_final: 0.7877 (m-10) REVERT: A 251 TYR cc_start: 0.8434 (OUTLIER) cc_final: 0.7413 (t80) outliers start: 5 outliers final: 1 residues processed: 62 average time/residue: 0.6866 time to fit residues: 43.8821 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 : 0.116 ------------------------------------------------------------------------------- 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: 5.9990 chunk 10 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 16 optimal weight: 0.9980 chunk 18 optimal weight: 0.5980 chunk 38 optimal weight: 0.7980 chunk 11 optimal weight: 0.8980 chunk 32 optimal weight: 4.9990 chunk 25 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.096695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.075313 restraints weight = 7488.276| |-----------------------------------------------------------------------------| r_work (start): 0.2858 rms_B_bonded: 2.68 r_work: 0.2717 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.2030 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= 0.148 Angle : 0.464 5.371 5890 Z= 0.264 Chirality : 0.033 0.116 634 Planarity : 0.003 0.023 712 Dihedral : 8.332 53.947 720 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 1.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 0.92 % Allowed : 19.12 % Favored : 79.95 % 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 aren not related in a simple way. whole: 4.78 (0.38), residues: 506 helix: 4.24 (0.24), residues: 402 sheet: None (None), residues: 0 loop : -1.79 (0.56), residues: 104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 292 TYR 0.009 0.001 TYR U 216 PHE 0.008 0.001 PHE U 259 TRP 0.007 0.001 TRP U 95 HIS 0.003 0.000 HIS A 64 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 4420) covalent geometry : angle 0.46434 ( 5890) hydrogen bonds : bond 0.07330 ( 330) hydrogen bonds : angle 2.95203 ( 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 : 0.103 Fit side-chains REVERT: U 190 TRP cc_start: 0.7911 (m-10) cc_final: 0.7566 (m-10) REVERT: U 251 TYR cc_start: 0.8490 (OUTLIER) cc_final: 0.7741 (t80) REVERT: A 55 GLU cc_start: 0.9048 (tp30) cc_final: 0.8743 (tp30) outliers start: 4 outliers final: 2 residues processed: 54 average time/residue: 0.6182 time to fit residues: 34.4969 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 : 0.163 ------------------------------------------------------------------------------- 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 251 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 21 optimal weight: 0.0070 chunk 5 optimal weight: 0.5980 chunk 10 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 39 optimal weight: 5.9990 chunk 34 optimal weight: 0.6980 chunk 27 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 overall best weight: 0.6000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.099042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.077327 restraints weight = 7495.876| |-----------------------------------------------------------------------------| r_work (start): 0.2912 rms_B_bonded: 2.71 r_work: 0.2774 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.2171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 4420 Z= 0.131 Angle : 0.438 5.341 5890 Z= 0.250 Chirality : 0.032 0.114 634 Planarity : 0.002 0.023 712 Dihedral : 7.762 58.046 720 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 2.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 0.69 % Allowed : 19.59 % Favored : 79.72 % 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 aren not related in a simple way. whole: 4.86 (0.38), residues: 506 helix: 4.27 (0.24), residues: 404 sheet: None (None), residues: 0 loop : -1.80 (0.56), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG U 292 TYR 0.007 0.001 TYR U 30 PHE 0.007 0.001 PHE A 232 TRP 0.009 0.001 TRP U 95 HIS 0.002 0.000 HIS A 64 Details of bonding type rmsd covalent geometry : bond 0.00247 ( 4420) covalent geometry : angle 0.43818 ( 5890) hydrogen bonds : bond 0.06603 ( 330) hydrogen bonds : angle 2.80578 ( 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 56 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 53 time to evaluate : 0.160 Fit side-chains REVERT: U 190 TRP cc_start: 0.7853 (m-10) cc_final: 0.7584 (m-10) REVERT: U 251 TYR cc_start: 0.8510 (OUTLIER) cc_final: 0.7713 (t80) REVERT: A 55 GLU cc_start: 0.9061 (tp30) cc_final: 0.8666 (tp30) outliers start: 3 outliers final: 2 residues processed: 56 average time/residue: 0.6127 time to fit residues: 35.5106 Evaluate side-chains 54 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 51 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 251 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 29 optimal weight: 0.6980 chunk 11 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 32 optimal weight: 4.9990 chunk 36 optimal weight: 0.8980 chunk 13 optimal weight: 0.9980 chunk 40 optimal weight: 0.8980 chunk 28 optimal weight: 0.9980 chunk 49 optimal weight: 0.9990 chunk 33 optimal weight: 0.8980 chunk 0 optimal weight: 3.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.095985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.074285 restraints weight = 7641.965| |-----------------------------------------------------------------------------| r_work (start): 0.2858 rms_B_bonded: 2.72 r_work: 0.2722 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 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 0.025 4420 Z= 0.149 Angle : 0.465 5.373 5890 Z= 0.265 Chirality : 0.033 0.118 634 Planarity : 0.002 0.023 712 Dihedral : 7.905 57.295 720 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 1.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % 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 aren not related in a simple way. whole: 4.80 (0.38), residues: 506 helix: 4.27 (0.24), residues: 402 sheet: None (None), residues: 0 loop : -1.88 (0.54), residues: 104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG U 292 TYR 0.011 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 covalent geometry : bond 0.00303 ( 4420) covalent geometry : angle 0.46469 ( 5890) hydrogen bonds : bond 0.07377 ( 330) hydrogen bonds : angle 2.95951 ( 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 55 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 52 time to evaluate : 0.126 Fit side-chains REVERT: U 190 TRP cc_start: 0.7829 (m-10) cc_final: 0.7580 (m-10) REVERT: U 251 TYR cc_start: 0.8551 (OUTLIER) cc_final: 0.7757 (t80) REVERT: A 55 GLU cc_start: 0.9078 (tp30) cc_final: 0.8683 (tp30) outliers start: 3 outliers final: 2 residues processed: 55 average time/residue: 0.6213 time to fit residues: 35.2875 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 : 0.162 ------------------------------------------------------------------------------- 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: 2.9990 chunk 6 optimal weight: 0.9990 chunk 41 optimal weight: 0.7980 chunk 13 optimal weight: 0.8980 chunk 42 optimal weight: 0.8980 chunk 19 optimal weight: 0.6980 chunk 39 optimal weight: 0.8980 chunk 12 optimal weight: 0.9980 chunk 28 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.096402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.074729 restraints weight = 7633.055| |-----------------------------------------------------------------------------| r_work (start): 0.2866 rms_B_bonded: 2.71 r_work: 0.2729 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.2168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4420 Z= 0.148 Angle : 0.470 5.453 5890 Z= 0.267 Chirality : 0.033 0.114 634 Planarity : 0.002 0.022 712 Dihedral : 7.641 50.324 720 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 2.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 0.92 % Allowed : 18.89 % Favored : 80.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.78 (0.38), residues: 506 helix: 4.27 (0.24), residues: 402 sheet: None (None), residues: 0 loop : -1.96 (0.53), residues: 104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG U 292 TYR 0.013 0.001 TYR A 155 PHE 0.007 0.001 PHE U 259 TRP 0.013 0.001 TRP A 190 HIS 0.003 0.000 HIS A 64 Details of bonding type rmsd covalent geometry : bond 0.00299 ( 4420) covalent geometry : angle 0.47019 ( 5890) hydrogen bonds : bond 0.07243 ( 330) hydrogen bonds : angle 2.93979 ( 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 55 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 51 time to evaluate : 0.171 Fit side-chains REVERT: U 190 TRP cc_start: 0.7828 (m-10) cc_final: 0.7582 (m-10) REVERT: U 251 TYR cc_start: 0.8528 (OUTLIER) cc_final: 0.7719 (t80) outliers start: 4 outliers final: 3 residues processed: 54 average time/residue: 0.6630 time to fit residues: 36.9199 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 : 0.245 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain A 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: 1.9990 chunk 31 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 18 optimal weight: 0.2980 chunk 35 optimal weight: 0.7980 chunk 17 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 32 optimal weight: 5.9990 chunk 9 optimal weight: 1.9990 chunk 21 optimal weight: 0.3980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.096957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.075578 restraints weight = 7531.273| |-----------------------------------------------------------------------------| r_work (start): 0.2861 rms_B_bonded: 2.69 r_work: 0.2717 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 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 0.030 4420 Z= 0.147 Angle : 0.477 6.010 5890 Z= 0.271 Chirality : 0.033 0.125 634 Planarity : 0.002 0.021 712 Dihedral : 7.371 49.433 720 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 1.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 0.92 % Allowed : 19.12 % Favored : 79.95 % 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 aren not related in a simple way. whole: 4.77 (0.38), residues: 506 helix: 4.25 (0.24), residues: 404 sheet: None (None), residues: 0 loop : -2.05 (0.54), 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 0.007 0.001 PHE U 259 TRP 0.007 0.001 TRP U 95 HIS 0.003 0.000 HIS A 64 Details of bonding type rmsd covalent geometry : bond 0.00297 ( 4420) covalent geometry : angle 0.47691 ( 5890) hydrogen bonds : bond 0.07192 ( 330) hydrogen bonds : angle 2.92591 ( 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 55 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 51 time to evaluate : 0.197 Fit side-chains REVERT: U 190 TRP cc_start: 0.7831 (m-10) cc_final: 0.7593 (m-10) REVERT: U 251 TYR cc_start: 0.8468 (OUTLIER) cc_final: 0.7593 (t80) outliers start: 4 outliers final: 2 residues processed: 54 average time/residue: 0.6259 time to fit residues: 34.9830 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 : 0.153 ------------------------------------------------------------------------------- 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: 0.7980 chunk 24 optimal weight: 0.5980 chunk 8 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 14 optimal weight: 5.9990 chunk 34 optimal weight: 0.9990 chunk 27 optimal weight: 0.5980 chunk 10 optimal weight: 2.9990 chunk 2 optimal weight: 0.8980 chunk 30 optimal weight: 0.9980 chunk 31 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.098101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.076625 restraints weight = 7619.901| |-----------------------------------------------------------------------------| r_work (start): 0.2879 rms_B_bonded: 2.71 r_work: 0.2736 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.2335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4420 Z= 0.142 Angle : 0.490 7.051 5890 Z= 0.276 Chirality : 0.033 0.143 634 Planarity : 0.002 0.020 712 Dihedral : 6.756 39.082 718 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 1.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 0.69 % Allowed : 20.05 % Favored : 79.26 % 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 aren not related in a simple way. whole: 4.86 (0.38), residues: 506 helix: 4.32 (0.24), residues: 404 sheet: None (None), residues: 0 loop : -2.02 (0.54), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG U 292 TYR 0.015 0.001 TYR A 155 PHE 0.007 0.001 PHE A 232 TRP 0.008 0.001 TRP U 95 HIS 0.003 0.000 HIS A 64 Details of bonding type rmsd covalent geometry : bond 0.00287 ( 4420) covalent geometry : angle 0.48958 ( 5890) hydrogen bonds : bond 0.06859 ( 330) hydrogen bonds : angle 2.85430 ( 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: 3 poor density : 49 time to evaluate : 0.173 Fit side-chains REVERT: U 251 TYR cc_start: 0.8478 (OUTLIER) cc_final: 0.7572 (t80) outliers start: 3 outliers final: 1 residues processed: 52 average time/residue: 0.5987 time to fit residues: 32.2705 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 : 0.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 207 LEU Chi-restraints excluded: chain U residue 251 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 17 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 46 optimal weight: 0.5980 chunk 13 optimal weight: 0.8980 chunk 24 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 23 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.096089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.074114 restraints weight = 7545.687| |-----------------------------------------------------------------------------| r_work (start): 0.2859 rms_B_bonded: 2.73 r_work: 0.2715 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.2360 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= 0.152 Angle : 0.508 7.825 5890 Z= 0.286 Chirality : 0.033 0.144 634 Planarity : 0.002 0.021 712 Dihedral : 6.965 38.609 718 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 2.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 0.46 % Allowed : 20.51 % Favored : 79.03 % 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 aren not related in a simple way. whole: 4.80 (0.38), residues: 506 helix: 4.29 (0.24), residues: 404 sheet: None (None), residues: 0 loop : -2.09 (0.54), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG U 292 TYR 0.011 0.001 TYR A 155 PHE 0.007 0.001 PHE U 259 TRP 0.007 0.001 TRP U 95 HIS 0.003 0.000 HIS A 64 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 4420) covalent geometry : angle 0.50810 ( 5890) hydrogen bonds : bond 0.07183 ( 330) hydrogen bonds : angle 2.92447 ( 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 51 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 49 time to evaluate : 0.163 Fit side-chains revert: symmetry clash REVERT: U 190 TRP cc_start: 0.7913 (m-10) cc_final: 0.7663 (m-10) REVERT: U 251 TYR cc_start: 0.8516 (OUTLIER) cc_final: 0.7590 (t80) REVERT: A 191 LYS cc_start: 0.8801 (pptt) cc_final: 0.8472 (mptt) outliers start: 2 outliers final: 1 residues processed: 51 average time/residue: 0.6223 time to fit residues: 32.8685 Evaluate side-chains 50 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 48 time to evaluate : 0.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 207 LEU Chi-restraints excluded: chain U residue 251 TYR 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: 0.6980 chunk 33 optimal weight: 0.6980 chunk 45 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 chunk 27 optimal weight: 0.8980 chunk 38 optimal weight: 0.9990 chunk 16 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.097345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.075614 restraints weight = 7609.798| |-----------------------------------------------------------------------------| r_work (start): 0.2863 rms_B_bonded: 2.71 r_work: 0.2720 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.2370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4420 Z= 0.149 Angle : 0.511 8.733 5890 Z= 0.287 Chirality : 0.033 0.158 634 Planarity : 0.002 0.021 712 Dihedral : 6.929 38.022 718 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 2.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 0.69 % Allowed : 20.05 % Favored : 79.26 % 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 aren not related in a simple way. whole: 4.85 (0.38), residues: 506 helix: 4.33 (0.24), residues: 404 sheet: None (None), residues: 0 loop : -2.09 (0.54), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG U 83 TYR 0.008 0.001 TYR U 216 PHE 0.007 0.001 PHE A 232 TRP 0.007 0.001 TRP U 95 HIS 0.004 0.000 HIS A 64 Details of bonding type rmsd covalent geometry : bond 0.00308 ( 4420) covalent geometry : angle 0.51097 ( 5890) hydrogen bonds : bond 0.07049 ( 330) hydrogen bonds : angle 2.89312 ( 990) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1466.67 seconds wall clock time: 25 minutes 43.99 seconds (1543.99 seconds total)