Starting phenix.real_space_refine on Sat May 10 03:04:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bsn_44870/05_2025/9bsn_44870_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bsn_44870/05_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_44870/05_2025/9bsn_44870.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bsn_44870/05_2025/9bsn_44870.map" model { file = "/net/cci-nas-00/data/ceres_data/9bsn_44870/05_2025/9bsn_44870_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bsn_44870/05_2025/9bsn_44870_trim.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 3.69, per 1000 atoms: 0.85 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: 1.26 Conformation dependent library (CDL) restraints added in 470.4 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: 0.35 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: 1.09 Time building geometry restraints manager: 1.41 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: 1.310 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: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 15.230 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.020 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:11.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.570 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.012 0.001 TRP U 222 HIS 0.003 0.001 HIS U 77 PHE 0.012 0.001 PHE U 232 TYR 0.010 0.001 TYR U 229 ARG 0.003 0.000 ARG A 68 Details of bonding type rmsd hydrogen bonds : bond 0.11460 ( 330) hydrogen bonds : angle 3.54514 ( 990) covalent geometry : bond 0.00367 ( 4420) covalent geometry : angle 0.62331 ( 5890) *********************** 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 : 0.482 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: 1.4473 time to fit residues: 108.8636 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 : 0.467 ------------------------------------------------------------------------------- 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 42 optimal weight: 2.9990 chunk 37 optimal weight: 0.5980 chunk 21 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 20 optimal weight: 4.9990 chunk 39 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 chunk 29 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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 = 0.3169 r_free = 0.3169 target = 0.093151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2807 r_free = 0.2807 target = 0.071740 restraints weight = 7570.283| |-----------------------------------------------------------------------------| r_work (start): 0.2799 rms_B_bonded: 2.67 r_work: 0.2653 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.2653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.1620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 4420 Z= 0.182 Angle : 0.508 5.479 5890 Z= 0.288 Chirality : 0.034 0.119 634 Planarity : 0.003 0.025 712 Dihedral : 10.211 73.663 720 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 1.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 1.84 % Allowed : 17.28 % Favored : 80.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.53 (0.38), residues: 506 helix: 4.05 (0.24), residues: 402 sheet: None (None), residues: 0 loop : -1.82 (0.55), residues: 104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP U 95 HIS 0.004 0.001 HIS A 64 PHE 0.010 0.001 PHE U 259 TYR 0.009 0.001 TYR A 155 ARG 0.003 0.000 ARG A 68 Details of bonding type rmsd hydrogen bonds : bond 0.08546 ( 330) hydrogen bonds : angle 3.25109 ( 990) covalent geometry : bond 0.00391 ( 4420) covalent geometry : angle 0.50773 ( 5890) *********************** 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 79 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 71 time to evaluate : 0.440 Fit side-chains revert: symmetry clash REVERT: U 67 SER cc_start: 0.8190 (OUTLIER) cc_final: 0.7555 (p) REVERT: U 251 TYR cc_start: 0.8408 (OUTLIER) cc_final: 0.7712 (t80) REVERT: A 51 GLN cc_start: 0.8714 (tm-30) cc_final: 0.8513 (tm-30) REVERT: A 70 GLU cc_start: 0.8607 (mp0) cc_final: 0.8028 (mp0) REVERT: A 147 GLU cc_start: 0.8264 (tm-30) cc_final: 0.8058 (tm-30) REVERT: A 251 TYR cc_start: 0.8410 (OUTLIER) cc_final: 0.7576 (t80) outliers start: 8 outliers final: 2 residues processed: 76 average time/residue: 1.5174 time to fit residues: 118.6477 Evaluate side-chains 64 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 59 time to evaluate : 0.478 ------------------------------------------------------------------------------- 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 82 THR 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 1 optimal weight: 0.9990 chunk 33 optimal weight: 0.8980 chunk 23 optimal weight: 0.6980 chunk 25 optimal weight: 0.6980 chunk 12 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 chunk 24 optimal weight: 0.6980 chunk 41 optimal weight: 0.5980 chunk 31 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3245 r_free = 0.3245 target = 0.098606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.076856 restraints weight = 7422.960| |-----------------------------------------------------------------------------| r_work (start): 0.2883 rms_B_bonded: 2.70 r_work: 0.2741 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.1915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 4420 Z= 0.138 Angle : 0.446 5.456 5890 Z= 0.255 Chirality : 0.033 0.116 634 Planarity : 0.002 0.023 712 Dihedral : 8.755 62.631 720 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 1.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 1.38 % Allowed : 17.97 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.73 (0.38), residues: 506 helix: 4.19 (0.24), residues: 402 sheet: None (None), residues: 0 loop : -1.74 (0.57), residues: 104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP U 95 HIS 0.003 0.001 HIS A 64 PHE 0.008 0.001 PHE U 259 TYR 0.007 0.001 TYR U 30 ARG 0.004 0.000 ARG A 292 Details of bonding type rmsd hydrogen bonds : bond 0.07074 ( 330) hydrogen bonds : angle 2.89931 ( 990) covalent geometry : bond 0.00261 ( 4420) covalent geometry : angle 0.44604 ( 5890) *********************** 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 59 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 53 time to evaluate : 0.476 Fit side-chains REVERT: U 190 TRP cc_start: 0.7893 (m-10) cc_final: 0.7605 (m-10) REVERT: U 251 TYR cc_start: 0.8441 (OUTLIER) cc_final: 0.7761 (t80) REVERT: A 51 GLN cc_start: 0.8791 (tm-30) cc_final: 0.8579 (tm-30) REVERT: A 55 GLU cc_start: 0.9041 (tp30) cc_final: 0.8677 (tp30) REVERT: A 190 TRP cc_start: 0.8133 (m-10) cc_final: 0.7924 (m-10) REVERT: A 251 TYR cc_start: 0.8454 (OUTLIER) cc_final: 0.7355 (t80) outliers start: 6 outliers final: 1 residues processed: 57 average time/residue: 1.2315 time to fit residues: 72.9286 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 : 0.466 ------------------------------------------------------------------------------- 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 40 optimal weight: 0.0040 chunk 5 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 34 optimal weight: 0.5980 chunk 24 optimal weight: 0.5980 chunk 26 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 18 optimal weight: 0.2980 chunk 25 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 overall best weight: 0.4592 ------------------------------------------------------------------------------- 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 = 0.3295 r_free = 0.3295 target = 0.101198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.079707 restraints weight = 7581.577| |-----------------------------------------------------------------------------| r_work (start): 0.2949 rms_B_bonded: 2.68 r_work: 0.2817 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.2312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 4420 Z= 0.123 Angle : 0.428 5.379 5890 Z= 0.242 Chirality : 0.032 0.113 634 Planarity : 0.002 0.021 712 Dihedral : 7.657 57.745 720 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 2.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.89 (0.38), residues: 506 helix: 4.29 (0.24), residues: 404 sheet: None (None), residues: 0 loop : -1.77 (0.57), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP U 95 HIS 0.003 0.001 HIS A 64 PHE 0.007 0.001 PHE A 232 TYR 0.008 0.001 TYR U 30 ARG 0.004 0.000 ARG A 292 Details of bonding type rmsd hydrogen bonds : bond 0.06186 ( 330) hydrogen bonds : angle 2.69751 ( 990) covalent geometry : bond 0.00224 ( 4420) covalent geometry : angle 0.42850 ( 5890) *********************** 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 62 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 58 time to evaluate : 0.459 Fit side-chains REVERT: U 190 TRP cc_start: 0.7873 (m-10) cc_final: 0.7588 (m-10) REVERT: U 251 TYR cc_start: 0.8467 (OUTLIER) cc_final: 0.7792 (t80) REVERT: A 51 GLN cc_start: 0.8813 (tm-30) cc_final: 0.8595 (tm-30) REVERT: A 55 GLU cc_start: 0.9043 (tp30) cc_final: 0.8729 (tp30) REVERT: A 147 GLU cc_start: 0.8207 (tm-30) cc_final: 0.7987 (tm-30) outliers start: 4 outliers final: 2 residues processed: 61 average time/residue: 1.2107 time to fit residues: 76.6718 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 : 0.459 ------------------------------------------------------------------------------- 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 17 optimal weight: 0.7980 chunk 37 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 14 optimal weight: 4.9990 chunk 44 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 9 optimal weight: 0.9980 overall best weight: 1.1586 ------------------------------------------------------------------------------- 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 = 0.3186 r_free = 0.3186 target = 0.094211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2822 r_free = 0.2822 target = 0.072456 restraints weight = 7625.872| |-----------------------------------------------------------------------------| r_work (start): 0.2810 rms_B_bonded: 2.73 r_work: 0.2671 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.2029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 4420 Z= 0.172 Angle : 0.487 5.436 5890 Z= 0.277 Chirality : 0.034 0.121 634 Planarity : 0.003 0.023 712 Dihedral : 8.283 51.800 720 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 1.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.65 (0.38), residues: 506 helix: 4.22 (0.24), residues: 400 sheet: None (None), residues: 0 loop : -2.05 (0.54), residues: 106 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP U 95 HIS 0.004 0.001 HIS U 64 PHE 0.009 0.001 PHE U 259 TYR 0.012 0.001 TYR U 216 ARG 0.004 0.000 ARG U 292 Details of bonding type rmsd hydrogen bonds : bond 0.08162 ( 330) hydrogen bonds : angle 3.12402 ( 990) covalent geometry : bond 0.00368 ( 4420) covalent geometry : angle 0.48706 ( 5890) *********************** 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 55 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 51 time to evaluate : 0.440 Fit side-chains REVERT: U 190 TRP cc_start: 0.7900 (m-10) cc_final: 0.7634 (m-10) REVERT: U 251 TYR cc_start: 0.8567 (OUTLIER) cc_final: 0.7811 (t80) REVERT: A 51 GLN cc_start: 0.8874 (tm-30) cc_final: 0.8596 (tm-30) outliers start: 4 outliers final: 2 residues processed: 54 average time/residue: 1.3525 time to fit residues: 76.1159 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 : 0.409 ------------------------------------------------------------------------------- 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 1 optimal weight: 0.8980 chunk 20 optimal weight: 4.9990 chunk 37 optimal weight: 0.5980 chunk 18 optimal weight: 0.6980 chunk 32 optimal weight: 4.9990 chunk 39 optimal weight: 5.9990 chunk 34 optimal weight: 0.8980 chunk 31 optimal weight: 0.7980 chunk 15 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3232 r_free = 0.3232 target = 0.096986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.075312 restraints weight = 7563.898| |-----------------------------------------------------------------------------| r_work (start): 0.2873 rms_B_bonded: 2.70 r_work: 0.2736 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 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 0.025 4420 Z= 0.143 Angle : 0.454 5.382 5890 Z= 0.258 Chirality : 0.033 0.115 634 Planarity : 0.002 0.022 712 Dihedral : 7.544 50.839 720 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 2.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 0.69 % Allowed : 21.43 % Favored : 77.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.78 (0.38), residues: 506 helix: 4.26 (0.24), residues: 402 sheet: None (None), residues: 0 loop : -1.89 (0.54), residues: 104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP U 95 HIS 0.003 0.000 HIS A 64 PHE 0.007 0.001 PHE U 259 TYR 0.011 0.001 TYR A 155 ARG 0.004 0.000 ARG U 292 Details of bonding type rmsd hydrogen bonds : bond 0.07169 ( 330) hydrogen bonds : angle 2.92277 ( 990) covalent geometry : bond 0.00283 ( 4420) covalent geometry : angle 0.45395 ( 5890) *********************** 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 52 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 49 time to evaluate : 0.434 Fit side-chains REVERT: U 190 TRP cc_start: 0.7860 (m-10) cc_final: 0.7659 (m-10) REVERT: U 251 TYR cc_start: 0.8536 (OUTLIER) cc_final: 0.7725 (t80) REVERT: A 51 GLN cc_start: 0.8893 (tm-30) cc_final: 0.8609 (tm-30) outliers start: 3 outliers final: 2 residues processed: 52 average time/residue: 1.3121 time to fit residues: 70.7395 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 : 0.474 ------------------------------------------------------------------------------- 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 3 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 23 optimal weight: 0.8980 chunk 19 optimal weight: 0.9980 chunk 46 optimal weight: 0.9980 chunk 2 optimal weight: 0.8980 chunk 40 optimal weight: 2.9990 chunk 39 optimal weight: 4.9990 chunk 44 optimal weight: 3.9990 chunk 17 optimal weight: 0.9990 overall best weight: 0.9580 ------------------------------------------------------------------------------- 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 = 0.3211 r_free = 0.3211 target = 0.095616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.073951 restraints weight = 7519.105| |-----------------------------------------------------------------------------| r_work (start): 0.2848 rms_B_bonded: 2.69 r_work: 0.2709 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.2176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4420 Z= 0.155 Angle : 0.472 5.427 5890 Z= 0.268 Chirality : 0.033 0.116 634 Planarity : 0.002 0.022 712 Dihedral : 7.689 50.189 720 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 2.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.71 (0.38), residues: 506 helix: 4.23 (0.24), residues: 402 sheet: None (None), residues: 0 loop : -2.02 (0.53), residues: 104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 190 HIS 0.003 0.000 HIS A 64 PHE 0.008 0.001 PHE A 232 TYR 0.009 0.001 TYR U 216 ARG 0.004 0.000 ARG U 292 Details of bonding type rmsd hydrogen bonds : bond 0.07528 ( 330) hydrogen bonds : angle 3.00666 ( 990) covalent geometry : bond 0.00320 ( 4420) covalent geometry : angle 0.47219 ( 5890) *********************** 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 53 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 49 time to evaluate : 0.480 Fit side-chains REVERT: U 190 TRP cc_start: 0.7875 (m-10) cc_final: 0.7646 (m-10) REVERT: U 251 TYR cc_start: 0.8565 (OUTLIER) cc_final: 0.7664 (t80) REVERT: A 51 GLN cc_start: 0.8910 (tm-30) cc_final: 0.8617 (tm-30) outliers start: 4 outliers final: 1 residues processed: 53 average time/residue: 1.2041 time to fit residues: 66.3696 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 : 0.460 ------------------------------------------------------------------------------- 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 29 optimal weight: 3.9990 chunk 20 optimal weight: 0.0870 chunk 31 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 chunk 6 optimal weight: 0.7980 chunk 49 optimal weight: 0.6980 chunk 3 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 overall best weight: 0.6758 ------------------------------------------------------------------------------- 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 = 0.3232 r_free = 0.3232 target = 0.098438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.076719 restraints weight = 7435.473| |-----------------------------------------------------------------------------| r_work (start): 0.2889 rms_B_bonded: 2.70 r_work: 0.2748 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.2372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4420 Z= 0.136 Angle : 0.455 5.926 5890 Z= 0.258 Chirality : 0.033 0.124 634 Planarity : 0.002 0.020 712 Dihedral : 6.865 50.162 718 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 2.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.81 (0.38), residues: 506 helix: 4.28 (0.24), residues: 404 sheet: None (None), residues: 0 loop : -2.02 (0.54), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP U 95 HIS 0.002 0.000 HIS A 64 PHE 0.007 0.001 PHE A 232 TYR 0.013 0.001 TYR A 155 ARG 0.004 0.000 ARG U 292 Details of bonding type rmsd hydrogen bonds : bond 0.06734 ( 330) hydrogen bonds : angle 2.83970 ( 990) covalent geometry : bond 0.00263 ( 4420) covalent geometry : angle 0.45527 ( 5890) *********************** 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 51 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 47 time to evaluate : 0.514 Fit side-chains REVERT: U 190 TRP cc_start: 0.7834 (m-10) cc_final: 0.7615 (m-10) REVERT: U 251 TYR cc_start: 0.8479 (OUTLIER) cc_final: 0.7701 (t80) REVERT: A 51 GLN cc_start: 0.8833 (tm-30) cc_final: 0.8553 (tm-30) outliers start: 4 outliers final: 2 residues processed: 50 average time/residue: 1.1923 time to fit residues: 62.0415 Evaluate side-chains 48 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 45 time to evaluate : 0.448 ------------------------------------------------------------------------------- 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 30 optimal weight: 2.9990 chunk 49 optimal weight: 0.6980 chunk 21 optimal weight: 0.0570 chunk 47 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 28 optimal weight: 0.8980 chunk 35 optimal weight: 0.9990 chunk 2 optimal weight: 0.6980 chunk 13 optimal weight: 0.9980 chunk 44 optimal weight: 2.9990 chunk 12 optimal weight: 0.5980 overall best weight: 0.5898 ------------------------------------------------------------------------------- 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 = 0.3266 r_free = 0.3266 target = 0.100197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.078755 restraints weight = 7499.515| |-----------------------------------------------------------------------------| r_work (start): 0.2916 rms_B_bonded: 2.67 r_work: 0.2776 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.2517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4420 Z= 0.131 Angle : 0.465 7.345 5890 Z= 0.262 Chirality : 0.032 0.140 634 Planarity : 0.002 0.019 712 Dihedral : 6.537 55.575 718 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 2.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.88 (0.38), residues: 506 helix: 4.33 (0.24), residues: 404 sheet: None (None), residues: 0 loop : -2.00 (0.54), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP U 95 HIS 0.002 0.000 HIS A 64 PHE 0.007 0.001 PHE A 232 TYR 0.010 0.001 TYR A 155 ARG 0.004 0.000 ARG U 292 Details of bonding type rmsd hydrogen bonds : bond 0.06341 ( 330) hydrogen bonds : angle 2.75750 ( 990) covalent geometry : bond 0.00253 ( 4420) covalent geometry : angle 0.46472 ( 5890) *********************** 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 51 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 49 time to evaluate : 0.416 Fit side-chains REVERT: U 190 TRP cc_start: 0.7804 (m-10) cc_final: 0.7587 (m-10) REVERT: U 251 TYR cc_start: 0.8465 (OUTLIER) cc_final: 0.7612 (t80) REVERT: A 51 GLN cc_start: 0.8815 (tm-30) cc_final: 0.8570 (tm-30) outliers start: 2 outliers final: 1 residues processed: 51 average time/residue: 1.6720 time to fit residues: 88.1786 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 : 0.446 ------------------------------------------------------------------------------- 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 26 optimal weight: 3.9990 chunk 17 optimal weight: 0.9990 chunk 22 optimal weight: 0.9990 chunk 6 optimal weight: 0.7980 chunk 48 optimal weight: 0.7980 chunk 39 optimal weight: 4.9990 chunk 3 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 31 optimal weight: 0.7980 chunk 47 optimal weight: 0.8980 chunk 19 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3231 r_free = 0.3231 target = 0.097630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.076184 restraints weight = 7422.919| |-----------------------------------------------------------------------------| r_work (start): 0.2872 rms_B_bonded: 2.67 r_work: 0.2730 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.2426 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= 0.146 Angle : 0.509 8.256 5890 Z= 0.285 Chirality : 0.033 0.146 634 Planarity : 0.002 0.020 712 Dihedral : 6.887 57.945 718 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 2.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.83 (0.38), residues: 506 helix: 4.30 (0.24), residues: 404 sheet: None (None), residues: 0 loop : -2.05 (0.54), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP U 95 HIS 0.003 0.000 HIS A 64 PHE 0.007 0.001 PHE U 259 TYR 0.010 0.001 TYR A 155 ARG 0.003 0.000 ARG U 292 Details of bonding type rmsd hydrogen bonds : bond 0.06908 ( 330) hydrogen bonds : angle 2.86947 ( 990) covalent geometry : bond 0.00298 ( 4420) covalent geometry : angle 0.50894 ( 5890) ********************** 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 49 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 47 time to evaluate : 0.476 Fit side-chains REVERT: U 190 TRP cc_start: 0.7821 (m-10) cc_final: 0.7578 (m-10) REVERT: U 251 TYR cc_start: 0.8514 (OUTLIER) cc_final: 0.7681 (t80) REVERT: A 51 GLN cc_start: 0.8845 (tm-30) cc_final: 0.8574 (tm-30) outliers start: 2 outliers final: 1 residues processed: 49 average time/residue: 1.1280 time to fit residues: 57.6750 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 : 0.430 ------------------------------------------------------------------------------- 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 38 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 24 optimal weight: 0.5980 chunk 20 optimal weight: 0.8980 chunk 41 optimal weight: 0.5980 chunk 47 optimal weight: 2.9990 chunk 1 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 48 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.096215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.074398 restraints weight = 7551.454| |-----------------------------------------------------------------------------| r_work (start): 0.2854 rms_B_bonded: 2.71 r_work: 0.2711 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.2373 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= 0.150 Angle : 0.514 9.000 5890 Z= 0.288 Chirality : 0.033 0.158 634 Planarity : 0.002 0.020 712 Dihedral : 6.969 41.146 718 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 2.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 0.46 % Allowed : 21.66 % Favored : 77.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.83 (0.38), residues: 506 helix: 4.31 (0.24), residues: 404 sheet: None (None), residues: 0 loop : -2.06 (0.54), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP U 95 HIS 0.003 0.000 HIS A 64 PHE 0.007 0.001 PHE U 259 TYR 0.008 0.001 TYR U 216 ARG 0.003 0.000 ARG U 292 Details of bonding type rmsd hydrogen bonds : bond 0.07160 ( 330) hydrogen bonds : angle 2.90725 ( 990) covalent geometry : bond 0.00308 ( 4420) covalent geometry : angle 0.51410 ( 5890) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2943.87 seconds wall clock time: 51 minutes 35.38 seconds (3095.38 seconds total)