Starting phenix.real_space_refine on Wed Mar 4 00:49:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9k2z_62001/03_2026/9k2z_62001.cif Found real_map, /net/cci-nas-00/data/ceres_data/9k2z_62001/03_2026/9k2z_62001.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.78 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9k2z_62001/03_2026/9k2z_62001.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9k2z_62001/03_2026/9k2z_62001.map" model { file = "/net/cci-nas-00/data/ceres_data/9k2z_62001/03_2026/9k2z_62001.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9k2z_62001/03_2026/9k2z_62001.cif" } resolution = 2.78 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= -0.007 sd= 0.063 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: 6 Type Number sf(0) Gaussians P 347 5.49 5 Mg 4 5.21 5 S 7 5.16 5 C 4728 2.51 5 N 1756 2.21 5 O 2754 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9596 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 2203 Classifications: {'peptide': 262} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 252} Chain breaks: 2 Chain: "B" Number of atoms: 6670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 6670 Classifications: {'RNA': 313} Modifications used: {'rna2p_pur': 18, 'rna2p_pyr': 18, 'rna3p_pur': 155, 'rna3p_pyr': 122} Link IDs: {'rna2p': 35, 'rna3p': 277} Chain breaks: 2 Chain: "C" Number of atoms: 513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 513 Classifications: {'DNA': 25} Link IDs: {'rna3p': 24} Chain breaks: 1 Chain: "D" Number of atoms: 189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 189 Classifications: {'DNA': 9} Link IDs: {'rna3p': 8} Chain: "B" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 21 Unusual residues: {' MG': 4} Classifications: {'undetermined': 4, 'water': 17} Link IDs: {None: 20} Time building chain proxies: 1.82, per 1000 atoms: 0.19 Number of scatterers: 9596 At special positions: 0 Unit cell: (77.8125, 118.275, 161.85, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 7 16.00 P 347 15.00 Mg 4 11.99 O 2754 8.00 N 1756 7.00 C 4728 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: 0.77 Conformation dependent library (CDL) restraints added in 190.1 milliseconds 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 498 Finding SS restraints... Secondary structure from input PDB file: 5 helices and 3 sheets defined 25.2% alpha, 26.3% beta 128 base pairs and 227 stacking pairs defined. Time for finding SS restraints: 1.68 Creating SS restraints... Processing helix chain 'A' and resid 19 through 28 Processing helix chain 'A' and resid 93 through 110 Processing helix chain 'A' and resid 122 through 127 Processing helix chain 'A' and resid 132 through 150 removed outlier: 3.585A pdb=" N LYS A 138 " --> pdb=" O SER A 134 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL A 142 " --> pdb=" O LYS A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 286 removed outlier: 3.554A pdb=" N GLU A 284 " --> pdb=" O GLU A 280 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N LEU A 285 " --> pdb=" O ARG A 281 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 17 through 18 removed outlier: 6.031A pdb=" N VAL A 40 " --> pdb=" O LYS A 34 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 157 through 158 removed outlier: 6.556A pdb=" N GLN A 74 " --> pdb=" O VAL A 82 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N VAL A 82 " --> pdb=" O GLN A 74 " (cutoff:3.500A) removed outlier: 9.458A pdb=" N TRP A 329 " --> pdb=" O VAL A 83 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N LYS A 85 " --> pdb=" O TRP A 329 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N ILE A 331 " --> pdb=" O LYS A 85 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N THR A 87 " --> pdb=" O ILE A 331 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N GLU A 89 " --> pdb=" O PRO A 333 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 390 through 391 removed outlier: 7.079A pdb=" N ALA A 377 " --> pdb=" O LEU A 371 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N LEU A 371 " --> pdb=" O ALA A 377 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ASN A 379 " --> pdb=" O THR A 369 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N ASP A 352 " --> pdb=" O VAL A 368 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N SER A 355 " --> pdb=" O LEU A 397 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N LEU A 397 " --> pdb=" O SER A 355 " (cutoff:3.500A) 82 hydrogen bonds defined for protein. 234 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 310 hydrogen bonds 552 hydrogen bond angles 0 basepair planarities 128 basepair parallelities 227 stacking parallelities Total time for adding SS restraints: 2.11 Time building geometry restraints manager: 1.07 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: 1210 1.33 - 1.45: 4570 1.45 - 1.57: 4017 1.57 - 1.69: 694 1.69 - 1.81: 10 Bond restraints: 10501 Sorted by residual: bond pdb=" P A B 34 " pdb=" OP2 A B 34 " ideal model delta sigma weight residual 1.485 1.645 -0.160 2.00e-02 2.50e+03 6.41e+01 bond pdb=" P A B 34 " pdb=" OP1 A B 34 " ideal model delta sigma weight residual 1.485 1.581 -0.096 2.00e-02 2.50e+03 2.32e+01 bond pdb=" O5' A B 312 " pdb=" C5' A B 312 " ideal model delta sigma weight residual 1.420 1.471 -0.051 1.50e-02 4.44e+03 1.15e+01 bond pdb=" O5' U B 311 " pdb=" C5' U B 311 " ideal model delta sigma weight residual 1.420 1.470 -0.050 1.50e-02 4.44e+03 1.12e+01 bond pdb=" O5' G B 156 " pdb=" C5' G B 156 " ideal model delta sigma weight residual 1.420 1.470 -0.050 1.50e-02 4.44e+03 1.09e+01 ... (remaining 10496 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.06: 13659 2.06 - 4.12: 2004 4.12 - 6.17: 160 6.17 - 8.23: 23 8.23 - 10.29: 2 Bond angle restraints: 15848 Sorted by residual: angle pdb=" O2' G B 253 " pdb=" C2' G B 253 " pdb=" C1' G B 253 " ideal model delta sigma weight residual 108.40 116.95 -8.55 1.50e+00 4.44e-01 3.25e+01 angle pdb=" C LYS A 388 " pdb=" CA LYS A 388 " pdb=" CB LYS A 388 " ideal model delta sigma weight residual 110.42 120.71 -10.29 1.99e+00 2.53e-01 2.67e+01 angle pdb=" C4' A B 284 " pdb=" C3' A B 284 " pdb=" O3' A B 284 " ideal model delta sigma weight residual 113.00 105.56 7.44 1.50e+00 4.44e-01 2.46e+01 angle pdb=" CA ASP A 62 " pdb=" CB ASP A 62 " pdb=" CG ASP A 62 " ideal model delta sigma weight residual 112.60 117.39 -4.79 1.00e+00 1.00e+00 2.29e+01 angle pdb=" N TYR A 114 " pdb=" CA TYR A 114 " pdb=" CB TYR A 114 " ideal model delta sigma weight residual 109.83 116.86 -7.03 1.51e+00 4.39e-01 2.17e+01 ... (remaining 15843 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.50: 5256 19.50 - 39.00: 611 39.00 - 58.50: 310 58.50 - 78.00: 245 78.00 - 97.50: 4 Dihedral angle restraints: 6426 sinusoidal: 5652 harmonic: 774 Sorted by residual: dihedral pdb=" O4' A B 7 " pdb=" C1' A B 7 " pdb=" N9 A B 7 " pdb=" C4 A B 7 " ideal model delta sinusoidal sigma weight residual 68.00 148.96 -80.96 1 1.70e+01 3.46e-03 2.80e+01 dihedral pdb=" C LYS A 388 " pdb=" N LYS A 388 " pdb=" CA LYS A 388 " pdb=" CB LYS A 388 " ideal model delta harmonic sigma weight residual -122.60 -134.16 11.56 0 2.50e+00 1.60e-01 2.14e+01 dihedral pdb=" C5' G B 222 " pdb=" C4' G B 222 " pdb=" C3' G B 222 " pdb=" O3' G B 222 " ideal model delta sinusoidal sigma weight residual 82.00 112.43 -30.43 1 8.00e+00 1.56e-02 2.07e+01 ... (remaining 6423 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.214: 2003 0.214 - 0.429: 9 0.429 - 0.643: 4 0.643 - 0.858: 1 0.858 - 1.072: 1 Chirality restraints: 2018 Sorted by residual: chirality pdb=" P A B 34 " pdb=" OP1 A B 34 " pdb=" OP2 A B 34 " pdb=" O5' A B 34 " both_signs ideal model delta sigma weight residual True 2.41 3.48 -1.07 2.00e-01 2.50e+01 2.87e+01 chirality pdb=" P DG C 0 " pdb=" OP1 DG C 0 " pdb=" OP2 DG C 0 " pdb=" O5' DG C 0 " both_signs ideal model delta sigma weight residual True 2.35 2.99 -0.65 2.00e-01 2.50e+01 1.04e+01 chirality pdb=" P DG C -10 " pdb=" OP1 DG C -10 " pdb=" OP2 DG C -10 " pdb=" O5' DG C -10 " both_signs ideal model delta sigma weight residual True 2.35 -2.99 -0.64 2.00e-01 2.50e+01 1.03e+01 ... (remaining 2015 not shown) Planarity restraints: 725 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G B 207 " -0.042 2.00e-02 2.50e+03 1.72e-02 8.92e+00 pdb=" N9 G B 207 " 0.032 2.00e-02 2.50e+03 pdb=" C8 G B 207 " 0.008 2.00e-02 2.50e+03 pdb=" N7 G B 207 " 0.001 2.00e-02 2.50e+03 pdb=" C5 G B 207 " -0.003 2.00e-02 2.50e+03 pdb=" C6 G B 207 " -0.009 2.00e-02 2.50e+03 pdb=" O6 G B 207 " -0.005 2.00e-02 2.50e+03 pdb=" N1 G B 207 " -0.013 2.00e-02 2.50e+03 pdb=" C2 G B 207 " 0.005 2.00e-02 2.50e+03 pdb=" N2 G B 207 " 0.000 2.00e-02 2.50e+03 pdb=" N3 G B 207 " 0.017 2.00e-02 2.50e+03 pdb=" C4 G B 207 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U B 115 " -0.041 2.00e-02 2.50e+03 1.89e-02 8.06e+00 pdb=" N1 U B 115 " 0.027 2.00e-02 2.50e+03 pdb=" C2 U B 115 " 0.012 2.00e-02 2.50e+03 pdb=" O2 U B 115 " 0.009 2.00e-02 2.50e+03 pdb=" N3 U B 115 " -0.006 2.00e-02 2.50e+03 pdb=" C4 U B 115 " -0.010 2.00e-02 2.50e+03 pdb=" O4 U B 115 " -0.013 2.00e-02 2.50e+03 pdb=" C5 U B 115 " 0.008 2.00e-02 2.50e+03 pdb=" C6 U B 115 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A B 175 " 0.039 2.00e-02 2.50e+03 1.63e-02 7.28e+00 pdb=" N9 A B 175 " -0.027 2.00e-02 2.50e+03 pdb=" C8 A B 175 " -0.008 2.00e-02 2.50e+03 pdb=" N7 A B 175 " 0.000 2.00e-02 2.50e+03 pdb=" C5 A B 175 " -0.008 2.00e-02 2.50e+03 pdb=" C6 A B 175 " 0.006 2.00e-02 2.50e+03 pdb=" N6 A B 175 " 0.012 2.00e-02 2.50e+03 pdb=" N1 A B 175 " 0.009 2.00e-02 2.50e+03 pdb=" C2 A B 175 " -0.006 2.00e-02 2.50e+03 pdb=" N3 A B 175 " -0.012 2.00e-02 2.50e+03 pdb=" C4 A B 175 " -0.007 2.00e-02 2.50e+03 ... (remaining 722 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.50: 31 2.50 - 3.10: 5763 3.10 - 3.70: 17585 3.70 - 4.30: 26887 4.30 - 4.90: 34944 Nonbonded interactions: 85210 Sorted by model distance: nonbonded pdb=" OP1 U B 166 " pdb="MG MG B 404 " model vdw 1.898 2.170 nonbonded pdb="MG MG B 401 " pdb=" O HOH B 504 " model vdw 2.006 2.170 nonbonded pdb="MG MG B 401 " pdb=" O HOH B 508 " model vdw 2.020 2.170 nonbonded pdb="MG MG B 403 " pdb=" O HOH B 510 " model vdw 2.020 2.170 nonbonded pdb=" OP2 A B 146 " pdb="MG MG B 401 " model vdw 2.029 2.170 ... (remaining 85205 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: 2.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.090 Find NCS groups from input model: 0.030 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:9.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8939 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 : 0.011 0.160 10501 Z= 0.649 Angle : 1.404 10.291 15848 Z= 0.900 Chirality : 0.101 1.072 2018 Planarity : 0.006 0.057 725 Dihedral : 20.901 97.502 5928 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 0.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Cbeta Deviations : 0.40 % Peptide Plane: Cis-proline : 11.11 % 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: -2.41 (0.47), residues: 256 helix: -0.94 (0.59), residues: 58 sheet: -1.23 (0.61), residues: 76 loop : -2.13 (0.46), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.002 ARG A 122 TYR 0.015 0.002 TYR A 104 PHE 0.009 0.003 PHE A 380 TRP 0.009 0.003 TRP A 406 HIS 0.005 0.001 HIS A 96 Details of bonding type rmsd covalent geometry : bond 0.01060 (10501) covalent geometry : angle 1.40372 (15848) hydrogen bonds : bond 0.17741 ( 392) hydrogen bonds : angle 6.91651 ( 786) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 0.226 Fit side-chains revert: symmetry clash REVERT: A 56 ARG cc_start: 0.8343 (mmm160) cc_final: 0.8120 (mmm-85) REVERT: A 157 GLU cc_start: 0.7758 (mt-10) cc_final: 0.7038 (mt-10) outliers start: 0 outliers final: 1 residues processed: 49 average time/residue: 0.9433 time to fit residues: 48.2498 Evaluate side-chains 33 residues out of total 237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 32 time to evaluate : 0.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 54 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 48 optimal weight: 5.9990 chunk 56 optimal weight: 6.9990 chunk 26 optimal weight: 6.9990 chunk 2 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 32 optimal weight: 10.0000 chunk 31 optimal weight: 7.9990 chunk 25 optimal weight: 0.5980 chunk 58 optimal weight: 1.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 GLN A 116 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.107831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.069731 restraints weight = 21617.685| |-----------------------------------------------------------------------------| r_work (start): 0.3054 rms_B_bonded: 1.30 r_work: 0.2879 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2760 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8828 moved from start: 0.1963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.032 10501 Z= 0.309 Angle : 0.591 9.621 15848 Z= 0.315 Chirality : 0.038 0.229 2018 Planarity : 0.005 0.027 725 Dihedral : 21.268 95.998 5350 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.27 % Allowed : 9.70 % Favored : 89.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.27 (0.52), residues: 256 helix: 1.42 (0.63), residues: 59 sheet: -1.60 (0.57), residues: 85 loop : -1.36 (0.57), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 144 TYR 0.024 0.002 TYR A 356 PHE 0.012 0.002 PHE A 380 TRP 0.006 0.001 TRP A 399 HIS 0.003 0.001 HIS A 67 Details of bonding type rmsd covalent geometry : bond 0.00600 (10501) covalent geometry : angle 0.59092 (15848) hydrogen bonds : bond 0.05584 ( 392) hydrogen bonds : angle 3.47644 ( 786) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 42 time to evaluate : 0.165 Fit side-chains REVERT: A 50 ASP cc_start: 0.7009 (t0) cc_final: 0.6637 (t0) REVERT: A 56 ARG cc_start: 0.8587 (mmm160) cc_final: 0.8274 (mmm-85) REVERT: A 396 ARG cc_start: 0.8273 (ptt-90) cc_final: 0.8013 (ptt-90) outliers start: 3 outliers final: 3 residues processed: 43 average time/residue: 0.7121 time to fit residues: 32.4899 Evaluate side-chains 25 residues out of total 237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 22 time to evaluate : 0.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 ASP Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 408 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 39 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 chunk 16 optimal weight: 6.9990 chunk 1 optimal weight: 4.9990 chunk 46 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 chunk 43 optimal weight: 2.9990 chunk 21 optimal weight: 5.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 10 ASN A 11 ASN A 379 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.105519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.065496 restraints weight = 20302.139| |-----------------------------------------------------------------------------| r_work (start): 0.3066 rms_B_bonded: 1.30 r_work: 0.2895 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2776 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8819 moved from start: 0.2481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 10501 Z= 0.268 Angle : 0.528 7.066 15848 Z= 0.286 Chirality : 0.033 0.216 2018 Planarity : 0.004 0.038 725 Dihedral : 21.255 95.346 5350 Min Nonbonded Distance : 1.808 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.11 % Allowed : 10.97 % Favored : 86.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -0.84 (0.53), residues: 256 helix: 2.14 (0.62), residues: 59 sheet: -1.46 (0.56), residues: 85 loop : -1.21 (0.58), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 144 TYR 0.017 0.002 TYR A 405 PHE 0.010 0.001 PHE A 380 TRP 0.005 0.001 TRP A 399 HIS 0.005 0.001 HIS A 364 Details of bonding type rmsd covalent geometry : bond 0.00522 (10501) covalent geometry : angle 0.52805 (15848) hydrogen bonds : bond 0.05016 ( 392) hydrogen bonds : angle 3.36331 ( 786) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 24 time to evaluate : 0.136 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 106 ARG cc_start: 0.8584 (OUTLIER) cc_final: 0.8130 (mtt90) REVERT: A 396 ARG cc_start: 0.8233 (ptt-90) cc_final: 0.7910 (ptt-90) outliers start: 5 outliers final: 4 residues processed: 26 average time/residue: 1.0598 time to fit residues: 28.6963 Evaluate side-chains 27 residues out of total 237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 22 time to evaluate : 0.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 ASP Chi-restraints excluded: chain A residue 106 ARG Chi-restraints excluded: chain A residue 349 ARG Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 408 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 30 optimal weight: 10.0000 chunk 14 optimal weight: 0.9980 chunk 25 optimal weight: 0.8980 chunk 23 optimal weight: 10.0000 chunk 17 optimal weight: 9.9990 chunk 18 optimal weight: 0.7980 chunk 44 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 55 optimal weight: 10.0000 chunk 57 optimal weight: 10.0000 chunk 56 optimal weight: 8.9990 overall best weight: 1.9384 ------------------------------------------------------------------------------- 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 = 0.3833 r_free = 0.3833 target = 0.105906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.065897 restraints weight = 20480.335| |-----------------------------------------------------------------------------| r_work (start): 0.3075 rms_B_bonded: 1.28 r_work: 0.2906 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2787 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8833 moved from start: 0.2573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.028 10501 Z= 0.242 Angle : 0.512 5.285 15848 Z= 0.279 Chirality : 0.033 0.214 2018 Planarity : 0.005 0.057 725 Dihedral : 21.265 95.871 5350 Min Nonbonded Distance : 1.806 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.53 % Allowed : 12.66 % Favored : 84.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -0.55 (0.55), residues: 256 helix: 2.49 (0.64), residues: 59 sheet: -1.33 (0.58), residues: 85 loop : -1.07 (0.60), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 56 TYR 0.016 0.002 TYR A 405 PHE 0.012 0.002 PHE A 380 TRP 0.005 0.001 TRP A 399 HIS 0.003 0.001 HIS A 364 Details of bonding type rmsd covalent geometry : bond 0.00471 (10501) covalent geometry : angle 0.51216 (15848) hydrogen bonds : bond 0.04933 ( 392) hydrogen bonds : angle 3.30416 ( 786) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 22 time to evaluate : 0.165 Fit side-chains revert: symmetry clash REVERT: A 12 ARG cc_start: 0.8983 (mtp85) cc_final: 0.8651 (ttp80) REVERT: A 106 ARG cc_start: 0.8581 (OUTLIER) cc_final: 0.8148 (mtt90) REVERT: A 396 ARG cc_start: 0.8363 (ptt-90) cc_final: 0.8161 (ptt-90) outliers start: 6 outliers final: 4 residues processed: 25 average time/residue: 1.1080 time to fit residues: 28.8969 Evaluate side-chains 26 residues out of total 237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 21 time to evaluate : 0.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 106 ARG Chi-restraints excluded: chain A residue 349 ARG Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 408 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 25 optimal weight: 0.9980 chunk 53 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 56 optimal weight: 8.9990 chunk 35 optimal weight: 3.9990 chunk 54 optimal weight: 4.9990 chunk 52 optimal weight: 3.9990 chunk 4 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- 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 = 0.3835 r_free = 0.3835 target = 0.106027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.066204 restraints weight = 20439.739| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 1.27 r_work: 0.2917 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2800 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8823 moved from start: 0.2592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10501 Z= 0.224 Angle : 0.505 4.767 15848 Z= 0.276 Chirality : 0.032 0.209 2018 Planarity : 0.004 0.038 725 Dihedral : 21.254 96.065 5348 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 3.80 % Allowed : 12.24 % Favored : 83.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -0.45 (0.55), residues: 256 helix: 2.71 (0.64), residues: 59 sheet: -1.37 (0.58), residues: 85 loop : -0.99 (0.61), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 144 TYR 0.015 0.001 TYR A 405 PHE 0.011 0.002 PHE A 380 TRP 0.006 0.001 TRP A 399 HIS 0.003 0.001 HIS A 67 Details of bonding type rmsd covalent geometry : bond 0.00438 (10501) covalent geometry : angle 0.50480 (15848) hydrogen bonds : bond 0.04879 ( 392) hydrogen bonds : angle 3.28335 ( 786) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 20 time to evaluate : 0.167 Fit side-chains revert: symmetry clash REVERT: A 56 ARG cc_start: 0.8494 (mtp85) cc_final: 0.8057 (mmm-85) REVERT: A 106 ARG cc_start: 0.8554 (OUTLIER) cc_final: 0.8105 (mtt90) REVERT: A 396 ARG cc_start: 0.8313 (ptt-90) cc_final: 0.8110 (ptt-90) outliers start: 9 outliers final: 4 residues processed: 25 average time/residue: 1.1274 time to fit residues: 29.3187 Evaluate side-chains 25 residues out of total 237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 20 time to evaluate : 0.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 106 ARG Chi-restraints excluded: chain A residue 349 ARG Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 408 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 9 optimal weight: 2.9990 chunk 22 optimal weight: 6.9990 chunk 3 optimal weight: 0.7980 chunk 43 optimal weight: 3.9990 chunk 57 optimal weight: 10.0000 chunk 25 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 35 optimal weight: 3.9990 chunk 18 optimal weight: 0.9980 chunk 39 optimal weight: 3.9990 chunk 29 optimal weight: 20.0000 overall best weight: 1.5586 ------------------------------------------------------------------------------- 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 = 0.3845 r_free = 0.3845 target = 0.106497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.066697 restraints weight = 20514.574| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 1.26 r_work: 0.2927 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2810 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8800 moved from start: 0.2685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 10501 Z= 0.202 Angle : 0.500 8.488 15848 Z= 0.272 Chirality : 0.031 0.206 2018 Planarity : 0.004 0.037 725 Dihedral : 21.243 96.802 5348 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.69 % Allowed : 15.19 % Favored : 83.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -0.45 (0.55), residues: 256 helix: 2.73 (0.65), residues: 58 sheet: -1.46 (0.58), residues: 85 loop : -0.89 (0.61), residues: 113 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 12 TYR 0.014 0.001 TYR A 405 PHE 0.009 0.001 PHE A 380 TRP 0.005 0.001 TRP A 399 HIS 0.002 0.001 HIS A 108 Details of bonding type rmsd covalent geometry : bond 0.00394 (10501) covalent geometry : angle 0.49998 (15848) hydrogen bonds : bond 0.04729 ( 392) hydrogen bonds : angle 3.26605 ( 786) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 22 time to evaluate : 0.168 Fit side-chains revert: symmetry clash REVERT: A 280 GLU cc_start: 0.7521 (tm-30) cc_final: 0.6906 (tm-30) REVERT: A 284 GLU cc_start: 0.8138 (mp0) cc_final: 0.7526 (mp0) REVERT: A 396 ARG cc_start: 0.8295 (ptt-90) cc_final: 0.8066 (ptt-90) outliers start: 4 outliers final: 5 residues processed: 23 average time/residue: 1.1444 time to fit residues: 27.4246 Evaluate side-chains 26 residues out of total 237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 21 time to evaluate : 0.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 ASP Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 349 ARG Chi-restraints excluded: chain A residue 363 ILE Chi-restraints excluded: chain A residue 408 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 13 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 chunk 37 optimal weight: 4.9990 chunk 49 optimal weight: 4.9990 chunk 14 optimal weight: 0.7980 chunk 25 optimal weight: 0.9990 chunk 27 optimal weight: 4.9990 chunk 20 optimal weight: 0.9990 chunk 47 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- 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 = 0.3843 r_free = 0.3843 target = 0.106487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.066726 restraints weight = 20534.260| |-----------------------------------------------------------------------------| r_work (start): 0.3098 rms_B_bonded: 1.24 r_work: 0.2931 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2815 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8814 moved from start: 0.2719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 10501 Z= 0.202 Angle : 0.495 7.421 15848 Z= 0.270 Chirality : 0.031 0.204 2018 Planarity : 0.005 0.055 725 Dihedral : 21.238 97.088 5348 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.11 % Allowed : 15.61 % Favored : 82.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -0.45 (0.55), residues: 256 helix: 2.78 (0.66), residues: 58 sheet: -1.52 (0.57), residues: 85 loop : -0.86 (0.60), residues: 113 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 56 TYR 0.014 0.001 TYR A 405 PHE 0.009 0.001 PHE A 380 TRP 0.005 0.001 TRP A 399 HIS 0.002 0.001 HIS A 108 Details of bonding type rmsd covalent geometry : bond 0.00394 (10501) covalent geometry : angle 0.49547 (15848) hydrogen bonds : bond 0.04697 ( 392) hydrogen bonds : angle 3.22225 ( 786) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 21 time to evaluate : 0.118 Fit side-chains revert: symmetry clash REVERT: A 56 ARG cc_start: 0.8449 (mmm-85) cc_final: 0.8106 (mtp85) REVERT: A 106 ARG cc_start: 0.8569 (OUTLIER) cc_final: 0.8118 (mtt90) REVERT: A 280 GLU cc_start: 0.7605 (tm-30) cc_final: 0.6978 (tm-30) REVERT: A 284 GLU cc_start: 0.8164 (mp0) cc_final: 0.7595 (mp0) REVERT: A 396 ARG cc_start: 0.8303 (ptt-90) cc_final: 0.8085 (ptt-90) outliers start: 5 outliers final: 3 residues processed: 23 average time/residue: 1.3017 time to fit residues: 30.9606 Evaluate side-chains 25 residues out of total 237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 21 time to evaluate : 0.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 106 ARG Chi-restraints excluded: chain A residue 349 ARG Chi-restraints excluded: chain A residue 408 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 46 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 2 optimal weight: 5.9990 chunk 32 optimal weight: 10.0000 chunk 48 optimal weight: 5.9990 chunk 55 optimal weight: 8.9990 chunk 16 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 28 optimal weight: 6.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 120 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.104507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.064313 restraints weight = 20297.639| |-----------------------------------------------------------------------------| r_work (start): 0.3043 rms_B_bonded: 1.37 r_work: 0.2874 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2756 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8857 moved from start: 0.2704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.038 10501 Z= 0.358 Angle : 0.581 6.773 15848 Z= 0.312 Chirality : 0.038 0.236 2018 Planarity : 0.005 0.038 725 Dihedral : 21.321 96.929 5348 Min Nonbonded Distance : 1.775 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 2.11 % Allowed : 16.46 % Favored : 81.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -0.69 (0.54), residues: 256 helix: 2.44 (0.66), residues: 58 sheet: -1.63 (0.56), residues: 85 loop : -0.95 (0.59), residues: 113 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 56 TYR 0.016 0.002 TYR A 405 PHE 0.013 0.002 PHE A 380 TRP 0.007 0.002 TRP A 399 HIS 0.003 0.001 HIS A 108 Details of bonding type rmsd covalent geometry : bond 0.00699 (10501) covalent geometry : angle 0.58111 (15848) hydrogen bonds : bond 0.05588 ( 392) hydrogen bonds : angle 3.37986 ( 786) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 29 time to evaluate : 0.173 Fit side-chains REVERT: A 50 ASP cc_start: 0.7288 (t0) cc_final: 0.6781 (t0) REVERT: A 106 ARG cc_start: 0.8569 (OUTLIER) cc_final: 0.8170 (mtt90) REVERT: A 280 GLU cc_start: 0.7614 (tm-30) cc_final: 0.6984 (tm-30) REVERT: A 284 GLU cc_start: 0.8297 (mp0) cc_final: 0.7815 (mp0) REVERT: A 343 ASP cc_start: 0.8916 (t0) cc_final: 0.8326 (t0) REVERT: A 349 ARG cc_start: 0.8672 (OUTLIER) cc_final: 0.7653 (mtp180) REVERT: A 396 ARG cc_start: 0.8276 (ptt-90) cc_final: 0.8049 (ptt-90) outliers start: 5 outliers final: 3 residues processed: 31 average time/residue: 0.9180 time to fit residues: 29.7374 Evaluate side-chains 26 residues out of total 237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 21 time to evaluate : 0.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 ASP Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 106 ARG Chi-restraints excluded: chain A residue 349 ARG Chi-restraints excluded: chain A residue 408 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 2 optimal weight: 3.9990 chunk 28 optimal weight: 5.9990 chunk 9 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 45 optimal weight: 2.9990 chunk 31 optimal weight: 9.9990 chunk 34 optimal weight: 6.9990 chunk 35 optimal weight: 2.9990 chunk 25 optimal weight: 0.6980 chunk 7 optimal weight: 4.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- 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 = 0.3874 r_free = 0.3874 target = 0.108519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.070779 restraints weight = 21564.164| |-----------------------------------------------------------------------------| r_work (start): 0.3086 rms_B_bonded: 1.24 r_work: 0.2918 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2799 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8807 moved from start: 0.2770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 10501 Z= 0.205 Angle : 0.519 6.678 15848 Z= 0.283 Chirality : 0.032 0.206 2018 Planarity : 0.005 0.037 725 Dihedral : 21.358 97.424 5348 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.69 % Allowed : 17.30 % Favored : 81.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -0.66 (0.55), residues: 256 helix: 2.58 (0.66), residues: 58 sheet: -1.69 (0.57), residues: 85 loop : -0.93 (0.58), residues: 113 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 12 TYR 0.016 0.001 TYR A 405 PHE 0.009 0.001 PHE A 380 TRP 0.006 0.001 TRP A 399 HIS 0.002 0.001 HIS A 67 Details of bonding type rmsd covalent geometry : bond 0.00400 (10501) covalent geometry : angle 0.51912 (15848) hydrogen bonds : bond 0.05041 ( 392) hydrogen bonds : angle 3.30919 ( 786) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 21 time to evaluate : 0.117 Fit side-chains revert: symmetry clash REVERT: A 12 ARG cc_start: 0.9010 (mtp85) cc_final: 0.8643 (ttp80) REVERT: A 56 ARG cc_start: 0.8519 (mtp85) cc_final: 0.8151 (mmm-85) REVERT: A 106 ARG cc_start: 0.8584 (OUTLIER) cc_final: 0.8135 (mtt90) REVERT: A 280 GLU cc_start: 0.7564 (tm-30) cc_final: 0.6853 (tm-30) REVERT: A 284 GLU cc_start: 0.8342 (mp0) cc_final: 0.7960 (mp0) REVERT: A 396 ARG cc_start: 0.8302 (ptt-90) cc_final: 0.8069 (ptt-90) outliers start: 4 outliers final: 3 residues processed: 22 average time/residue: 1.2195 time to fit residues: 27.7917 Evaluate side-chains 25 residues out of total 237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 21 time to evaluate : 0.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 106 ARG Chi-restraints excluded: chain A residue 349 ARG Chi-restraints excluded: chain A residue 408 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 54 optimal weight: 5.9990 chunk 24 optimal weight: 7.9990 chunk 41 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 chunk 33 optimal weight: 20.0000 chunk 22 optimal weight: 3.9990 chunk 6 optimal weight: 0.4980 chunk 21 optimal weight: 7.9990 chunk 23 optimal weight: 5.9990 chunk 16 optimal weight: 2.9990 chunk 49 optimal weight: 4.9990 overall best weight: 3.0988 ------------------------------------------------------------------------------- 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 = 0.3811 r_free = 0.3811 target = 0.104543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.064342 restraints weight = 20341.765| |-----------------------------------------------------------------------------| r_work (start): 0.3046 rms_B_bonded: 1.37 r_work: 0.2876 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2754 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8860 moved from start: 0.2758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.039 10501 Z= 0.367 Angle : 0.570 6.500 15848 Z= 0.307 Chirality : 0.037 0.231 2018 Planarity : 0.005 0.038 725 Dihedral : 21.312 97.114 5348 Min Nonbonded Distance : 1.745 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 2.11 % Allowed : 16.88 % Favored : 81.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.74 (0.54), residues: 256 helix: 2.45 (0.67), residues: 58 sheet: -1.71 (0.57), residues: 85 loop : -0.97 (0.58), residues: 113 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 144 TYR 0.015 0.002 TYR A 405 PHE 0.014 0.002 PHE A 380 TRP 0.006 0.002 TRP A 399 HIS 0.003 0.001 HIS A 108 Details of bonding type rmsd covalent geometry : bond 0.00715 (10501) covalent geometry : angle 0.57038 (15848) hydrogen bonds : bond 0.05452 ( 392) hydrogen bonds : angle 3.36588 ( 786) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 22 time to evaluate : 0.154 Fit side-chains revert: symmetry clash REVERT: A 106 ARG cc_start: 0.8579 (OUTLIER) cc_final: 0.8176 (mtt90) REVERT: A 280 GLU cc_start: 0.7593 (tm-30) cc_final: 0.6927 (tm-30) REVERT: A 284 GLU cc_start: 0.8349 (mp0) cc_final: 0.7966 (mp0) REVERT: A 396 ARG cc_start: 0.8325 (ptt-90) cc_final: 0.8081 (ptt-90) outliers start: 5 outliers final: 4 residues processed: 24 average time/residue: 1.1127 time to fit residues: 27.7421 Evaluate side-chains 26 residues out of total 237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 21 time to evaluate : 0.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 ASP Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 106 ARG Chi-restraints excluded: chain A residue 349 ARG Chi-restraints excluded: chain A residue 408 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 11 optimal weight: 0.8980 chunk 25 optimal weight: 0.6980 chunk 20 optimal weight: 3.9990 chunk 28 optimal weight: 5.9990 chunk 50 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 34 optimal weight: 6.9990 chunk 31 optimal weight: 8.9990 chunk 21 optimal weight: 8.9990 chunk 10 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- 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 = 0.3834 r_free = 0.3834 target = 0.105877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.065980 restraints weight = 20299.848| |-----------------------------------------------------------------------------| r_work (start): 0.3080 rms_B_bonded: 1.26 r_work: 0.2913 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2796 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8821 moved from start: 0.2830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10501 Z= 0.203 Angle : 0.514 6.481 15848 Z= 0.280 Chirality : 0.031 0.206 2018 Planarity : 0.005 0.051 725 Dihedral : 21.343 97.741 5348 Min Nonbonded Distance : 1.807 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.69 % Allowed : 16.88 % Favored : 81.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -0.64 (0.54), residues: 256 helix: 2.54 (0.67), residues: 58 sheet: -1.68 (0.57), residues: 85 loop : -0.88 (0.58), residues: 113 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 56 TYR 0.015 0.001 TYR A 405 PHE 0.009 0.001 PHE A 380 TRP 0.006 0.001 TRP A 399 HIS 0.002 0.001 HIS A 96 Details of bonding type rmsd covalent geometry : bond 0.00395 (10501) covalent geometry : angle 0.51356 (15848) hydrogen bonds : bond 0.04887 ( 392) hydrogen bonds : angle 3.28439 ( 786) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3537.63 seconds wall clock time: 60 minutes 51.97 seconds (3651.97 seconds total)