Starting phenix.real_space_refine on Fri Sep 11 02:55:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jfp_61435/09_2026/9jfp_61435.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jfp_61435/09_2026/9jfp_61435.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9jfp_61435/09_2026/9jfp_61435.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jfp_61435/09_2026/9jfp_61435.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9jfp_61435/09_2026/9jfp_61435.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jfp_61435/09_2026/9jfp_61435.map" } resolution = 2.96 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= 0.061 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 P 164 5.49 5 S 15 5.16 5 C 3743 2.51 5 N 1273 2.21 5 O 1726 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6921 Number of models: 1 Model: "" Number of chains: 4 Chain: "C" Number of atoms: 329 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 329 Classifications: {'DNA': 16} Link IDs: {'rna3p': 15} Chain: "D" Number of atoms: 285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 285 Classifications: {'DNA': 14} Link IDs: {'rna3p': 13} Chain: "F" Number of atoms: 2875 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 2875 Classifications: {'RNA': 134} Modifications used: {'rna2p_pur': 10, 'rna2p_pyr': 5, 'rna3p_pur': 67, 'rna3p_pyr': 52} Link IDs: {'rna2p': 15, 'rna3p': 118} Chain breaks: 2 Chain: "A" Number of atoms: 3432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3432 Classifications: {'peptide': 431} Link IDs: {'PTRANS': 24, 'TRANS': 406} Chain breaks: 1 Time building chain proxies: 1.60, per 1000 atoms: 0.23 Number of scatterers: 6921 At special positions: 0 Unit cell: (103.726, 94.4496, 118.062, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 15 16.00 P 164 15.00 O 1726 8.00 N 1273 7.00 C 3743 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: 0.56 Conformation dependent library (CDL) restraints added in 254.8 milliseconds 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 822 Finding SS restraints... Secondary structure from input PDB file: 17 helices and 3 sheets defined 45.5% alpha, 10.9% beta 57 base pairs and 91 stacking pairs defined. Time for finding SS restraints: 0.89 Creating SS restraints... Processing helix chain 'A' and resid 26 through 51 Processing helix chain 'A' and resid 52 through 54 No H-bonds generated for 'chain 'A' and resid 52 through 54' Processing helix chain 'A' and resid 72 through 77 Processing helix chain 'A' and resid 77 through 88 removed outlier: 3.607A pdb=" N ARG A 81 " --> pdb=" O ASN A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 95 Proline residue: A 95 - end of helix Processing helix chain 'A' and resid 96 through 101 Processing helix chain 'A' and resid 108 through 117 removed outlier: 3.664A pdb=" N LYS A 112 " --> pdb=" O SER A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 150 No H-bonds generated for 'chain 'A' and resid 148 through 150' Processing helix chain 'A' and resid 191 through 198 Processing helix chain 'A' and resid 272 through 277 removed outlier: 3.897A pdb=" N ASP A 276 " --> pdb=" O GLN A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 289 Processing helix chain 'A' and resid 299 through 319 Processing helix chain 'A' and resid 339 through 375 removed outlier: 3.666A pdb=" N ILE A 345 " --> pdb=" O ARG A 341 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LYS A 374 " --> pdb=" O GLU A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 388 Processing helix chain 'A' and resid 394 through 399 Processing helix chain 'A' and resid 402 through 415 removed outlier: 3.928A pdb=" N PHE A 406 " --> pdb=" O ALA A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 478 Processing sheet with id=AA1, first strand: chain 'A' and resid 9 through 13 Processing sheet with id=AA2, first strand: chain 'A' and resid 142 through 147 removed outlier: 4.244A pdb=" N THR A 206 " --> pdb=" O THR A 222 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N LYS A 174 " --> pdb=" O TYR A 24 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 252 through 253 removed outlier: 7.331A pdb=" N TYR A 268 " --> pdb=" O ILE A 259 " (cutoff:3.500A) 158 hydrogen bonds defined for protein. 450 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 147 hydrogen bonds 278 hydrogen bond angles 0 basepair planarities 57 basepair parallelities 91 stacking parallelities Total time for adding SS restraints: 1.27 Time building geometry restraints manager: 0.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 1377 1.33 - 1.45: 2499 1.45 - 1.57: 3180 1.57 - 1.69: 322 1.69 - 1.81: 26 Bond restraints: 7404 Sorted by residual: bond pdb=" O3' C F 21 " pdb=" P A F 22 " ideal model delta sigma weight residual 1.607 1.559 0.048 1.20e-02 6.94e+03 1.59e+01 bond pdb=" C3' DT C 17 " pdb=" C2' DT C 17 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.07e+00 bond pdb=" C3' DC D 10 " pdb=" C2' DC D 10 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.29e+00 bond pdb=" C3' DT D 6 " pdb=" C2' DT D 6 " ideal model delta sigma weight residual 1.516 1.538 -0.022 8.00e-03 1.56e+04 7.49e+00 bond pdb=" C3' DT D 7 " pdb=" C2' DT D 7 " ideal model delta sigma weight residual 1.516 1.534 -0.018 8.00e-03 1.56e+04 4.98e+00 ... (remaining 7399 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.77: 10165 1.77 - 3.53: 589 3.53 - 5.30: 25 5.30 - 7.06: 3 7.06 - 8.83: 3 Bond angle restraints: 10785 Sorted by residual: angle pdb=" O5' A F 22 " pdb=" C5' A F 22 " pdb=" C4' A F 22 " ideal model delta sigma weight residual 109.40 113.44 -4.04 8.00e-01 1.56e+00 2.55e+01 angle pdb=" O4' DC C 28 " pdb=" C4' DC C 28 " pdb=" C3' DC C 28 " ideal model delta sigma weight residual 106.00 103.01 2.99 6.00e-01 2.78e+00 2.49e+01 angle pdb=" C3' U F 23 " pdb=" C2' U F 23 " pdb=" C1' U F 23 " ideal model delta sigma weight residual 101.50 104.99 -3.49 8.00e-01 1.56e+00 1.90e+01 angle pdb=" O4' U F 23 " pdb=" C1' U F 23 " pdb=" C2' U F 23 " ideal model delta sigma weight residual 105.80 110.08 -4.28 1.00e+00 1.00e+00 1.83e+01 angle pdb=" N3 DT C 17 " pdb=" C4 DT C 17 " pdb=" O4 DT C 17 " ideal model delta sigma weight residual 119.90 122.47 -2.57 6.00e-01 2.78e+00 1.83e+01 ... (remaining 10780 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.53: 3992 35.53 - 71.07: 514 71.07 - 106.60: 49 106.60 - 142.14: 3 142.14 - 177.67: 4 Dihedral angle restraints: 4562 sinusoidal: 3297 harmonic: 1265 Sorted by residual: dihedral pdb=" O4' C F 88 " pdb=" C1' C F 88 " pdb=" N1 C F 88 " pdb=" C2 C F 88 " ideal model delta sinusoidal sigma weight residual -128.00 49.67 -177.67 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' U F 23 " pdb=" C2' U F 23 " pdb=" C1' U F 23 " pdb=" C3' U F 23 " ideal model delta sinusoidal sigma weight residual -35.00 2.87 -37.87 1 8.00e+00 1.56e-02 3.16e+01 dihedral pdb=" C4' U F 23 " pdb=" C3' U F 23 " pdb=" C2' U F 23 " pdb=" C1' U F 23 " ideal model delta sinusoidal sigma weight residual -35.00 2.17 -37.17 1 8.00e+00 1.56e-02 3.05e+01 ... (remaining 4559 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 1107 0.083 - 0.166: 183 0.166 - 0.249: 6 0.249 - 0.332: 1 0.332 - 0.415: 1 Chirality restraints: 1298 Sorted by residual: chirality pdb=" C3' G F 77 " pdb=" C4' G F 77 " pdb=" O3' G F 77 " pdb=" C2' G F 77 " both_signs ideal model delta sigma weight residual False -2.74 -2.33 -0.41 2.00e-01 2.50e+01 4.30e+00 chirality pdb=" C3' C F 76 " pdb=" C4' C F 76 " pdb=" O3' C F 76 " pdb=" C2' C F 76 " both_signs ideal model delta sigma weight residual False -2.74 -2.43 -0.32 2.00e-01 2.50e+01 2.48e+00 chirality pdb=" P G F 24 " pdb=" OP1 G F 24 " pdb=" OP2 G F 24 " pdb=" O5' G F 24 " both_signs ideal model delta sigma weight residual True 2.41 -2.62 -0.21 2.00e-01 2.50e+01 1.07e+00 ... (remaining 1295 not shown) Planarity restraints: 779 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G F 77 " -0.024 2.00e-02 2.50e+03 1.19e-02 4.25e+00 pdb=" N9 G F 77 " 0.024 2.00e-02 2.50e+03 pdb=" C8 G F 77 " 0.004 2.00e-02 2.50e+03 pdb=" N7 G F 77 " -0.005 2.00e-02 2.50e+03 pdb=" C5 G F 77 " 0.008 2.00e-02 2.50e+03 pdb=" C6 G F 77 " 0.001 2.00e-02 2.50e+03 pdb=" O6 G F 77 " -0.015 2.00e-02 2.50e+03 pdb=" N1 G F 77 " 0.002 2.00e-02 2.50e+03 pdb=" C2 G F 77 " 0.005 2.00e-02 2.50e+03 pdb=" N2 G F 77 " 0.001 2.00e-02 2.50e+03 pdb=" N3 G F 77 " -0.010 2.00e-02 2.50e+03 pdb=" C4 G F 77 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U F 23 " -0.025 2.00e-02 2.50e+03 1.23e-02 3.43e+00 pdb=" N1 U F 23 " 0.021 2.00e-02 2.50e+03 pdb=" C2 U F 23 " 0.008 2.00e-02 2.50e+03 pdb=" O2 U F 23 " 0.001 2.00e-02 2.50e+03 pdb=" N3 U F 23 " -0.001 2.00e-02 2.50e+03 pdb=" C4 U F 23 " -0.009 2.00e-02 2.50e+03 pdb=" O4 U F 23 " -0.004 2.00e-02 2.50e+03 pdb=" C5 U F 23 " -0.002 2.00e-02 2.50e+03 pdb=" C6 U F 23 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U F 84 " -0.020 2.00e-02 2.50e+03 1.18e-02 3.15e+00 pdb=" N1 U F 84 " 0.029 2.00e-02 2.50e+03 pdb=" C2 U F 84 " -0.002 2.00e-02 2.50e+03 pdb=" O2 U F 84 " 0.002 2.00e-02 2.50e+03 pdb=" N3 U F 84 " -0.002 2.00e-02 2.50e+03 pdb=" C4 U F 84 " -0.003 2.00e-02 2.50e+03 pdb=" O4 U F 84 " -0.004 2.00e-02 2.50e+03 pdb=" C5 U F 84 " -0.000 2.00e-02 2.50e+03 pdb=" C6 U F 84 " 0.000 2.00e-02 2.50e+03 ... (remaining 776 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1382 2.78 - 3.31: 6260 3.31 - 3.84: 13367 3.84 - 4.37: 15153 4.37 - 4.90: 21883 Nonbonded interactions: 58045 Sorted by model distance: nonbonded pdb=" O2' U F 87 " pdb=" O2' U F 90 " model vdw 2.249 3.040 nonbonded pdb=" O ALA A 97 " pdb=" OG1 THR A 101 " model vdw 2.258 3.040 nonbonded pdb=" NE2 GLN A 32 " pdb=" O LYS A 168 " model vdw 2.311 3.120 nonbonded pdb=" OP2 U F 158 " pdb=" OG SER A 26 " model vdw 2.337 3.040 nonbonded pdb=" O2' G F 5 " pdb=" OP1 G F 6 " model vdw 2.346 3.040 ... (remaining 58040 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 1.760 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: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 8.330 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6675 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 0.048 7404 Z= 0.297 Angle : 0.761 8.829 10785 Z= 0.617 Chirality : 0.056 0.415 1298 Planarity : 0.004 0.040 779 Dihedral : 24.317 177.673 3740 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.42), residues: 427 helix: 1.16 (0.42), residues: 176 sheet: -0.53 (0.61), residues: 75 loop : -1.21 (0.45), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 141 TYR 0.014 0.001 TYR A 412 PHE 0.017 0.001 PHE A 143 TRP 0.005 0.001 TRP A 292 HIS 0.006 0.001 HIS A 365 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.30 ( 7404) covalent geometry : angle 0.76122 / 0.62 (10785) hydrogen bonds : bond 0.12640 / 15.21 ( 305) hydrogen bonds : angle 4.98066 / 6.21 ( 728) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 0.173 Fit side-chains REVERT: A 388 MET cc_start: 0.3144 (ptp) cc_final: 0.2793 (mmp) outliers start: 0 outliers final: 0 residues processed: 73 average time/residue: 0.5454 time to fit residues: 42.0022 Evaluate side-chains 42 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 54 optimal weight: 5.9990 chunk 24 optimal weight: 0.9980 chunk 48 optimal weight: 0.9980 chunk 56 optimal weight: 0.0470 chunk 26 optimal weight: 0.1980 chunk 2 optimal weight: 6.9990 chunk 16 optimal weight: 0.6980 chunk 32 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 50 optimal weight: 0.5980 overall best weight: 0.4478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 102 ASN A 190 HIS A 365 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4739 r_free = 0.4739 target = 0.256081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4377 r_free = 0.4377 target = 0.215074 restraints weight = 7494.575| |-----------------------------------------------------------------------------| r_work (start): 0.4375 rms_B_bonded: 1.99 r_work: 0.3782 rms_B_bonded: 4.78 restraints_weight: 0.5000 r_work (final): 0.3782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7301 moved from start: 0.1034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7404 Z= 0.133 Angle : 0.596 9.290 10785 Z= 0.331 Chirality : 0.042 0.421 1298 Planarity : 0.005 0.039 779 Dihedral : 25.933 178.809 2862 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 1.65 % Allowed : 13.77 % Favored : 84.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.42), residues: 427 helix: 1.37 (0.42), residues: 180 sheet: -0.46 (0.62), residues: 76 loop : -1.24 (0.45), residues: 171 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 141 TYR 0.031 0.002 TYR A 412 PHE 0.020 0.001 PHE A 143 TRP 0.004 0.001 TRP A 69 HIS 0.004 0.001 HIS A 190 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.13 ( 7404) covalent geometry : angle 0.59646 / 0.33 (10785) hydrogen bonds : bond 0.05620 / 6.32 ( 305) hydrogen bonds : angle 3.87824 / 5.28 ( 728) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 43 time to evaluate : 0.106 Fit side-chains REVERT: A 75 MET cc_start: 0.7092 (mtm) cc_final: 0.6360 (mtt) REVERT: A 203 ASN cc_start: 0.7870 (m110) cc_final: 0.7666 (m-40) REVERT: A 268 TYR cc_start: 0.6390 (m-80) cc_final: 0.5434 (m-80) REVERT: A 286 ARG cc_start: 0.7984 (mtm-85) cc_final: 0.7738 (mtm180) REVERT: A 388 MET cc_start: 0.3567 (ptp) cc_final: 0.3214 (mmp) outliers start: 6 outliers final: 3 residues processed: 48 average time/residue: 0.5233 time to fit residues: 26.6347 Evaluate side-chains 39 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 36 time to evaluate : 0.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 224 SER Chi-restraints excluded: chain A residue 351 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 33 optimal weight: 5.9990 chunk 54 optimal weight: 5.9990 chunk 41 optimal weight: 3.9990 chunk 12 optimal weight: 40.0000 chunk 34 optimal weight: 0.7980 chunk 43 optimal weight: 0.5980 chunk 39 optimal weight: 10.0000 chunk 56 optimal weight: 0.7980 chunk 51 optimal weight: 0.8980 chunk 50 optimal weight: 0.6980 chunk 13 optimal weight: 6.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 67 ASN ** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4706 r_free = 0.4706 target = 0.252234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.201258 restraints weight = 7344.657| |-----------------------------------------------------------------------------| r_work (start): 0.4239 rms_B_bonded: 1.36 r_work: 0.3773 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7349 moved from start: 0.1676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7404 Z= 0.142 Angle : 0.582 9.000 10785 Z= 0.321 Chirality : 0.041 0.421 1298 Planarity : 0.005 0.037 779 Dihedral : 25.796 178.289 2862 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 4.68 % Allowed : 13.50 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.42), residues: 427 helix: 1.42 (0.42), residues: 179 sheet: -0.59 (0.62), residues: 76 loop : -1.11 (0.46), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 358 TYR 0.033 0.002 TYR A 412 PHE 0.022 0.002 PHE A 143 TRP 0.020 0.002 TRP A 183 HIS 0.003 0.001 HIS A 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.14 ( 7404) covalent geometry : angle 0.58183 / 0.32 (10785) hydrogen bonds : bond 0.05099 / 5.79 ( 305) hydrogen bonds : angle 3.64430 / 5.10 ( 728) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 40 time to evaluate : 0.169 Fit side-chains revert: symmetry clash REVERT: A 132 ARG cc_start: 0.7033 (OUTLIER) cc_final: 0.6588 (tpt170) REVERT: A 182 ILE cc_start: 0.6326 (pp) cc_final: 0.6030 (mp) REVERT: A 268 TYR cc_start: 0.6387 (m-80) cc_final: 0.5433 (m-80) REVERT: A 353 GLU cc_start: 0.6843 (OUTLIER) cc_final: 0.5997 (tt0) REVERT: A 388 MET cc_start: 0.3582 (ptp) cc_final: 0.3281 (mmp) outliers start: 17 outliers final: 7 residues processed: 52 average time/residue: 0.6056 time to fit residues: 33.1832 Evaluate side-chains 46 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 37 time to evaluate : 0.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 132 ARG Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 224 SER Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 337 GLN Chi-restraints excluded: chain A residue 351 LYS Chi-restraints excluded: chain A residue 353 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 52 optimal weight: 20.0000 chunk 44 optimal weight: 4.9990 chunk 49 optimal weight: 0.8980 chunk 29 optimal weight: 0.1980 chunk 1 optimal weight: 5.9990 chunk 57 optimal weight: 4.9990 chunk 11 optimal weight: 10.0000 chunk 16 optimal weight: 0.9980 chunk 56 optimal weight: 7.9990 chunk 30 optimal weight: 0.4980 chunk 32 optimal weight: 0.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4721 r_free = 0.4721 target = 0.253534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.200432 restraints weight = 7464.491| |-----------------------------------------------------------------------------| r_work (start): 0.4238 rms_B_bonded: 1.36 r_work: 0.3773 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7389 moved from start: 0.1978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7404 Z= 0.136 Angle : 0.573 9.369 10785 Z= 0.313 Chirality : 0.041 0.409 1298 Planarity : 0.005 0.037 779 Dihedral : 25.777 177.814 2862 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 3.31 % Allowed : 16.80 % Favored : 79.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.42), residues: 427 helix: 1.55 (0.43), residues: 176 sheet: -0.53 (0.61), residues: 75 loop : -1.22 (0.44), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 290 TYR 0.025 0.002 TYR A 412 PHE 0.020 0.002 PHE A 143 TRP 0.005 0.001 TRP A 114 HIS 0.003 0.001 HIS A 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.14 ( 7404) covalent geometry : angle 0.57279 / 0.31 (10785) hydrogen bonds : bond 0.04660 / 5.23 ( 305) hydrogen bonds : angle 3.53921 / 5.00 ( 728) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 37 time to evaluate : 0.170 Fit side-chains revert: symmetry clash REVERT: A 75 MET cc_start: 0.7205 (mtm) cc_final: 0.6603 (mtt) REVERT: A 132 ARG cc_start: 0.6984 (OUTLIER) cc_final: 0.6561 (tpt-90) REVERT: A 182 ILE cc_start: 0.6278 (OUTLIER) cc_final: 0.5931 (mp) REVERT: A 268 TYR cc_start: 0.6327 (m-80) cc_final: 0.5344 (m-80) REVERT: A 353 GLU cc_start: 0.6913 (OUTLIER) cc_final: 0.6027 (tt0) REVERT: A 388 MET cc_start: 0.3737 (ptp) cc_final: 0.3417 (mmp) outliers start: 12 outliers final: 6 residues processed: 44 average time/residue: 0.6029 time to fit residues: 28.0220 Evaluate side-chains 44 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 35 time to evaluate : 0.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 132 ARG Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 224 SER Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 351 LYS Chi-restraints excluded: chain A residue 353 GLU Chi-restraints excluded: chain A residue 403 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 46 optimal weight: 0.0070 chunk 22 optimal weight: 1.9990 chunk 53 optimal weight: 9.9990 chunk 37 optimal weight: 0.5980 chunk 30 optimal weight: 0.0470 chunk 18 optimal weight: 0.7980 chunk 6 optimal weight: 9.9990 chunk 45 optimal weight: 0.9980 chunk 9 optimal weight: 50.0000 chunk 25 optimal weight: 1.9990 chunk 14 optimal weight: 7.9990 overall best weight: 0.4896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 272 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4727 r_free = 0.4727 target = 0.254310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.203028 restraints weight = 7496.730| |-----------------------------------------------------------------------------| r_work (start): 0.4259 rms_B_bonded: 1.39 r_work: 0.3777 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7364 moved from start: 0.2169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 7404 Z= 0.117 Angle : 0.548 9.311 10785 Z= 0.300 Chirality : 0.039 0.395 1298 Planarity : 0.004 0.037 779 Dihedral : 25.696 177.982 2862 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 3.58 % Allowed : 19.01 % Favored : 77.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.42), residues: 427 helix: 1.61 (0.43), residues: 176 sheet: -0.70 (0.61), residues: 76 loop : -1.15 (0.44), residues: 175 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 291 TYR 0.024 0.002 TYR A 412 PHE 0.017 0.001 PHE A 143 TRP 0.004 0.001 TRP A 235 HIS 0.002 0.000 HIS A 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00221 / 0.12 ( 7404) covalent geometry : angle 0.54824 / 0.30 (10785) hydrogen bonds : bond 0.04476 / 4.95 ( 305) hydrogen bonds : angle 3.41103 / 4.87 ( 728) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 38 time to evaluate : 0.183 Fit side-chains REVERT: A 75 MET cc_start: 0.7322 (mtm) cc_final: 0.6751 (mtt) REVERT: A 132 ARG cc_start: 0.7001 (OUTLIER) cc_final: 0.6560 (tpt-90) REVERT: A 182 ILE cc_start: 0.6140 (pp) cc_final: 0.5800 (mp) REVERT: A 268 TYR cc_start: 0.6544 (m-80) cc_final: 0.5443 (m-80) REVERT: A 353 GLU cc_start: 0.6865 (OUTLIER) cc_final: 0.6034 (tt0) REVERT: A 388 MET cc_start: 0.3718 (ptp) cc_final: 0.3495 (mmp) outliers start: 13 outliers final: 5 residues processed: 48 average time/residue: 0.5524 time to fit residues: 28.0939 Evaluate side-chains 38 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 31 time to evaluate : 0.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 132 ARG Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 351 LYS Chi-restraints excluded: chain A residue 353 GLU Chi-restraints excluded: chain A residue 403 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 2 optimal weight: 6.9990 chunk 51 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 chunk 35 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 chunk 1 optimal weight: 6.9990 chunk 9 optimal weight: 50.0000 chunk 4 optimal weight: 20.0000 chunk 54 optimal weight: 4.9990 chunk 15 optimal weight: 0.5980 chunk 21 optimal weight: 0.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 109 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4679 r_free = 0.4679 target = 0.248693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.201356 restraints weight = 7457.372| |-----------------------------------------------------------------------------| r_work (start): 0.4261 rms_B_bonded: 2.19 r_work (final): 0.4261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6720 moved from start: 0.2535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7404 Z= 0.167 Angle : 0.608 9.311 10785 Z= 0.333 Chirality : 0.043 0.442 1298 Planarity : 0.005 0.037 779 Dihedral : 25.711 178.064 2862 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 3.58 % Allowed : 19.56 % Favored : 76.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.42), residues: 427 helix: 1.39 (0.42), residues: 176 sheet: -0.67 (0.61), residues: 75 loop : -1.18 (0.44), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 358 TYR 0.027 0.002 TYR A 412 PHE 0.027 0.003 PHE A 143 TRP 0.008 0.002 TRP A 235 HIS 0.003 0.001 HIS A 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.17 ( 7404) covalent geometry : angle 0.60830 / 0.33 (10785) hydrogen bonds : bond 0.05010 / 5.72 ( 305) hydrogen bonds : angle 3.65491 / 5.16 ( 728) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 35 time to evaluate : 0.151 Fit side-chains REVERT: A 132 ARG cc_start: 0.6892 (OUTLIER) cc_final: 0.6358 (tpt170) REVERT: A 182 ILE cc_start: 0.6370 (OUTLIER) cc_final: 0.6119 (mt) REVERT: A 268 TYR cc_start: 0.6692 (m-80) cc_final: 0.6335 (m-80) REVERT: A 353 GLU cc_start: 0.6822 (OUTLIER) cc_final: 0.5996 (tt0) outliers start: 13 outliers final: 5 residues processed: 43 average time/residue: 0.5030 time to fit residues: 22.9843 Evaluate side-chains 43 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 35 time to evaluate : 0.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 ARG Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 337 GLN Chi-restraints excluded: chain A residue 351 LYS Chi-restraints excluded: chain A residue 353 GLU Chi-restraints excluded: chain A residue 403 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 22 optimal weight: 0.9990 chunk 20 optimal weight: 4.9990 chunk 17 optimal weight: 0.6980 chunk 23 optimal weight: 1.9990 chunk 8 optimal weight: 50.0000 chunk 49 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 53 optimal weight: 0.0670 chunk 9 optimal weight: 50.0000 chunk 51 optimal weight: 0.8980 chunk 10 optimal weight: 9.9990 overall best weight: 0.7322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 102 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4700 r_free = 0.4700 target = 0.251232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.198106 restraints weight = 7423.366| |-----------------------------------------------------------------------------| r_work (start): 0.4206 rms_B_bonded: 1.43 r_work: 0.3740 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7418 moved from start: 0.2649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7404 Z= 0.134 Angle : 0.570 9.393 10785 Z= 0.310 Chirality : 0.040 0.397 1298 Planarity : 0.004 0.037 779 Dihedral : 25.707 177.874 2862 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.03 % Favored : 92.97 % Rotamer: Outliers : 3.03 % Allowed : 21.21 % Favored : 75.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.42), residues: 427 helix: 1.42 (0.42), residues: 177 sheet: -0.81 (0.60), residues: 75 loop : -1.23 (0.44), residues: 175 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 358 TYR 0.020 0.002 TYR A 412 PHE 0.019 0.002 PHE A 143 TRP 0.006 0.001 TRP A 114 HIS 0.003 0.001 HIS A 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.13 ( 7404) covalent geometry : angle 0.56968 / 0.31 (10785) hydrogen bonds : bond 0.04472 / 5.00 ( 305) hydrogen bonds : angle 3.52208 / 5.06 ( 728) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 33 time to evaluate : 0.119 Fit side-chains REVERT: A 182 ILE cc_start: 0.6219 (OUTLIER) cc_final: 0.5947 (mp) REVERT: A 268 TYR cc_start: 0.6537 (m-80) cc_final: 0.5521 (m-80) REVERT: A 349 ARG cc_start: 0.7520 (OUTLIER) cc_final: 0.6897 (ttm170) REVERT: A 353 GLU cc_start: 0.6902 (OUTLIER) cc_final: 0.6013 (tt0) outliers start: 11 outliers final: 3 residues processed: 39 average time/residue: 0.5359 time to fit residues: 22.1196 Evaluate side-chains 39 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 33 time to evaluate : 0.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 ARG Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 349 ARG Chi-restraints excluded: chain A residue 353 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 40 optimal weight: 0.0770 chunk 24 optimal weight: 0.9980 chunk 10 optimal weight: 9.9990 chunk 29 optimal weight: 0.8980 chunk 6 optimal weight: 9.9990 chunk 3 optimal weight: 6.9990 chunk 5 optimal weight: 50.0000 chunk 47 optimal weight: 0.0670 chunk 55 optimal weight: 0.9990 chunk 35 optimal weight: 0.0970 chunk 8 optimal weight: 50.0000 overall best weight: 0.4274 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4711 r_free = 0.4711 target = 0.252617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.199557 restraints weight = 7461.544| |-----------------------------------------------------------------------------| r_work (start): 0.4222 rms_B_bonded: 1.44 r_work: 0.3749 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7406 moved from start: 0.2743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 7404 Z= 0.118 Angle : 0.557 9.551 10785 Z= 0.303 Chirality : 0.039 0.388 1298 Planarity : 0.004 0.038 779 Dihedral : 25.676 178.105 2862 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.03 % Favored : 92.97 % Rotamer: Outliers : 2.20 % Allowed : 21.76 % Favored : 76.03 % 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 are not related in a simple way. whole: -0.05 (0.42), residues: 427 helix: 1.42 (0.42), residues: 177 sheet: -0.81 (0.61), residues: 75 loop : -1.16 (0.44), residues: 175 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 275 TYR 0.018 0.001 TYR A 412 PHE 0.015 0.001 PHE A 143 TRP 0.005 0.001 TRP A 114 HIS 0.002 0.001 HIS A 365 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.12 ( 7404) covalent geometry : angle 0.55748 / 0.30 (10785) hydrogen bonds : bond 0.04220 / 4.70 ( 305) hydrogen bonds : angle 3.41464 / 4.90 ( 728) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 34 time to evaluate : 0.186 Fit side-chains REVERT: A 182 ILE cc_start: 0.6160 (OUTLIER) cc_final: 0.5882 (mp) REVERT: A 268 TYR cc_start: 0.6426 (m-80) cc_final: 0.5410 (m-80) REVERT: A 353 GLU cc_start: 0.6872 (OUTLIER) cc_final: 0.6009 (tt0) outliers start: 8 outliers final: 3 residues processed: 38 average time/residue: 0.5164 time to fit residues: 20.9075 Evaluate side-chains 39 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 34 time to evaluate : 0.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 353 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 18 optimal weight: 1.9990 chunk 5 optimal weight: 50.0000 chunk 14 optimal weight: 7.9990 chunk 30 optimal weight: 0.3980 chunk 57 optimal weight: 5.9990 chunk 36 optimal weight: 0.8980 chunk 53 optimal weight: 4.9990 chunk 56 optimal weight: 0.9990 chunk 31 optimal weight: 0.7980 chunk 42 optimal weight: 1.9990 chunk 13 optimal weight: 6.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 102 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4686 r_free = 0.4686 target = 0.249587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.198527 restraints weight = 7418.516| |-----------------------------------------------------------------------------| r_work (start): 0.4215 rms_B_bonded: 1.36 r_work: 0.3687 rms_B_bonded: 4.54 restraints_weight: 0.5000 r_work (final): 0.3687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7486 moved from start: 0.2929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7404 Z= 0.157 Angle : 0.595 9.556 10785 Z= 0.322 Chirality : 0.042 0.405 1298 Planarity : 0.005 0.037 779 Dihedral : 25.650 177.914 2862 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.26 % Favored : 92.74 % Rotamer: Outliers : 1.93 % Allowed : 22.31 % Favored : 75.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.42), residues: 427 helix: 1.36 (0.42), residues: 176 sheet: -0.77 (0.61), residues: 75 loop : -1.15 (0.44), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 358 TYR 0.024 0.002 TYR A 412 PHE 0.025 0.002 PHE A 143 TRP 0.011 0.002 TRP A 235 HIS 0.003 0.001 HIS A 119 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.16 ( 7404) covalent geometry : angle 0.59520 / 0.32 (10785) hydrogen bonds : bond 0.04589 / 5.23 ( 305) hydrogen bonds : angle 3.54348 / 5.07 ( 728) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 31 time to evaluate : 0.110 Fit side-chains REVERT: A 182 ILE cc_start: 0.6294 (OUTLIER) cc_final: 0.6008 (mp) REVERT: A 268 TYR cc_start: 0.6581 (m-80) cc_final: 0.5574 (m-80) REVERT: A 353 GLU cc_start: 0.6980 (OUTLIER) cc_final: 0.6131 (tt0) REVERT: A 388 MET cc_start: 0.4014 (mmp) cc_final: 0.2812 (ptp) outliers start: 7 outliers final: 2 residues processed: 35 average time/residue: 0.4753 time to fit residues: 17.8217 Evaluate side-chains 34 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 30 time to evaluate : 0.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 353 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 3 optimal weight: 6.9990 chunk 2 optimal weight: 6.9990 chunk 48 optimal weight: 0.0570 chunk 24 optimal weight: 0.0060 chunk 46 optimal weight: 0.0470 chunk 16 optimal weight: 0.9980 chunk 28 optimal weight: 0.9990 chunk 34 optimal weight: 0.8980 chunk 9 optimal weight: 50.0000 chunk 5 optimal weight: 50.0000 chunk 35 optimal weight: 0.5980 overall best weight: 0.3212 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4718 r_free = 0.4718 target = 0.253481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.199438 restraints weight = 7445.616| |-----------------------------------------------------------------------------| r_work (start): 0.4225 rms_B_bonded: 1.37 r_work: 0.3792 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7368 moved from start: 0.2982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 7404 Z= 0.112 Angle : 0.561 9.870 10785 Z= 0.303 Chirality : 0.038 0.384 1298 Planarity : 0.004 0.038 779 Dihedral : 25.610 178.152 2862 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 1.10 % Allowed : 23.14 % Favored : 75.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.42), residues: 427 helix: 1.39 (0.42), residues: 177 sheet: -0.78 (0.62), residues: 75 loop : -1.14 (0.45), residues: 175 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 291 TYR 0.015 0.001 TYR A 412 PHE 0.013 0.001 PHE A 143 TRP 0.018 0.002 TRP A 235 HIS 0.004 0.001 HIS A 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00211 / 0.11 ( 7404) covalent geometry : angle 0.56125 / 0.30 (10785) hydrogen bonds : bond 0.04061 / 4.50 ( 305) hydrogen bonds : angle 3.37883 / 4.83 ( 728) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 34 time to evaluate : 0.171 Fit side-chains REVERT: A 182 ILE cc_start: 0.5999 (OUTLIER) cc_final: 0.5742 (mp) REVERT: A 268 TYR cc_start: 0.6437 (m-80) cc_final: 0.5408 (m-80) REVERT: A 353 GLU cc_start: 0.6857 (OUTLIER) cc_final: 0.6004 (tt0) REVERT: A 388 MET cc_start: 0.4232 (mmp) cc_final: 0.2888 (ptp) outliers start: 4 outliers final: 2 residues processed: 36 average time/residue: 0.4660 time to fit residues: 18.0344 Evaluate side-chains 37 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 33 time to evaluate : 0.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 353 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 44 optimal weight: 10.0000 chunk 35 optimal weight: 1.9990 chunk 3 optimal weight: 7.9990 chunk 46 optimal weight: 3.9990 chunk 47 optimal weight: 0.8980 chunk 27 optimal weight: 0.0570 chunk 38 optimal weight: 0.8980 chunk 20 optimal weight: 0.6980 chunk 51 optimal weight: 3.9990 chunk 50 optimal weight: 0.8980 chunk 9 optimal weight: 50.0000 overall best weight: 0.6898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4700 r_free = 0.4700 target = 0.251136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.198741 restraints weight = 7442.422| |-----------------------------------------------------------------------------| r_work (start): 0.4214 rms_B_bonded: 1.40 r_work: 0.3708 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.3708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7450 moved from start: 0.3085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7404 Z= 0.133 Angle : 0.570 9.818 10785 Z= 0.308 Chirality : 0.040 0.394 1298 Planarity : 0.004 0.037 779 Dihedral : 25.566 178.104 2862 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.26 % Favored : 92.74 % Rotamer: Outliers : 1.65 % Allowed : 23.69 % Favored : 74.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.42), residues: 427 helix: 1.32 (0.42), residues: 177 sheet: -0.89 (0.61), residues: 76 loop : -1.18 (0.45), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 291 TYR 0.021 0.002 TYR A 412 PHE 0.021 0.002 PHE A 143 TRP 0.015 0.002 TRP A 235 HIS 0.004 0.001 HIS A 119 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.13 ( 7404) covalent geometry : angle 0.57022 / 0.31 (10785) hydrogen bonds : bond 0.04247 / 4.80 ( 305) hydrogen bonds : angle 3.45254 / 4.91 ( 728) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2044.06 seconds wall clock time: 35 minutes 43.15 seconds (2143.15 seconds total)