Starting phenix.real_space_refine on Wed Sep 17 03:59:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xcs_38253/09_2025/8xcs_38253.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xcs_38253/09_2025/8xcs_38253.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.63 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8xcs_38253/09_2025/8xcs_38253.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xcs_38253/09_2025/8xcs_38253.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8xcs_38253/09_2025/8xcs_38253.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xcs_38253/09_2025/8xcs_38253.map" } resolution = 2.63 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= 0.000 sd= 0.002 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 3 5.49 5 S 14 5.16 5 C 2121 2.51 5 N 567 2.21 5 O 655 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-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3360 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3281 Classifications: {'peptide': 418} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 397} Chain: "A" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 79 Unusual residues: {'AKG': 1, 'NDP': 1, 'NH4': 1} Classifications: {'undetermined': 3, 'water': 20} Link IDs: {None: 22} Time building chain proxies: 1.14, per 1000 atoms: 0.34 Number of scatterers: 3360 At special positions: 0 Unit cell: (71.44, 69.184, 68.432, 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 14 16.00 P 3 15.00 O 655 8.00 N 567 7.00 C 2121 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: 0.35 Conformation dependent library (CDL) restraints added in 139.1 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 762 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 3 sheets defined 55.5% alpha, 18.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.11 Creating SS restraints... Processing helix chain 'A' and resid 5 through 19 Processing helix chain 'A' and resid 24 through 32 Processing helix chain 'A' and resid 79 through 97 removed outlier: 3.815A pdb=" N VAL A 97 " --> pdb=" O LYS A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 115 Processing helix chain 'A' and resid 116 through 132 Processing helix chain 'A' and resid 133 through 135 No H-bonds generated for 'chain 'A' and resid 133 through 135' Processing helix chain 'A' and resid 149 through 165 Processing helix chain 'A' and resid 169 through 174 removed outlier: 3.919A pdb=" N ILE A 174 " --> pdb=" O PHE A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 207 Processing helix chain 'A' and resid 223 through 234 Processing helix chain 'A' and resid 256 through 268 Processing helix chain 'A' and resid 280 through 286 Processing helix chain 'A' and resid 305 through 309 removed outlier: 3.512A pdb=" N ILE A 309 " --> pdb=" O ALA A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 333 Processing helix chain 'A' and resid 339 through 344 Processing helix chain 'A' and resid 344 through 361 removed outlier: 4.472A pdb=" N VAL A 348 " --> pdb=" O ASN A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 392 Processing helix chain 'A' and resid 394 through 415 removed outlier: 3.762A pdb=" N SER A 405 " --> pdb=" O VAL A 401 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ARG A 406 " --> pdb=" O VAL A 402 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 36 through 45 removed outlier: 6.652A pdb=" N GLY A 103 " --> pdb=" O HIS A 61 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 36 through 45 removed outlier: 6.652A pdb=" N GLY A 103 " --> pdb=" O HIS A 61 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N LYS A 69 " --> pdb=" O GLY A 104 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N GLY A 106 " --> pdb=" O LYS A 69 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N THR A 68 " --> pdb=" O ILE A 141 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 277 through 279 removed outlier: 6.471A pdb=" N ILE A 215 " --> pdb=" O VAL A 239 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ALA A 241 " --> pdb=" O ILE A 215 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER A 243 " --> pdb=" O VAL A 217 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N LYS A 214 " --> pdb=" O VAL A 291 " (cutoff:3.500A) removed outlier: 7.922A pdb=" N ALA A 293 " --> pdb=" O LYS A 214 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ALA A 216 " --> pdb=" O ALA A 293 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N LEU A 292 " --> pdb=" O ALA A 315 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N VAL A 314 " --> pdb=" O ILE A 338 " (cutoff:3.500A) 199 hydrogen bonds defined for protein. 570 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.49 Time building geometry restraints manager: 0.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1004 1.34 - 1.45: 483 1.45 - 1.57: 1899 1.57 - 1.69: 2 1.69 - 1.81: 27 Bond restraints: 3415 Sorted by residual: bond pdb=" O1N NDP A 501 " pdb=" PN NDP A 501 " ideal model delta sigma weight residual 1.477 1.550 -0.073 1.00e-02 1.00e+04 5.28e+01 bond pdb=" O2B NDP A 501 " pdb=" P2B NDP A 501 " ideal model delta sigma weight residual 1.833 1.566 0.267 3.80e-02 6.93e+02 4.94e+01 bond pdb=" O5D NDP A 501 " pdb=" PN NDP A 501 " ideal model delta sigma weight residual 1.757 1.559 0.198 3.50e-02 8.16e+02 3.22e+01 bond pdb=" C1 AKG A 502 " pdb=" C2 AKG A 502 " ideal model delta sigma weight residual 1.559 1.461 0.098 2.00e-02 2.50e+03 2.39e+01 bond pdb=" C6A NDP A 501 " pdb=" N1A NDP A 501 " ideal model delta sigma weight residual 1.368 1.253 0.115 2.90e-02 1.19e+03 1.58e+01 ... (remaining 3410 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.42: 4600 4.42 - 8.85: 23 8.85 - 13.27: 10 13.27 - 17.69: 4 17.69 - 22.12: 1 Bond angle restraints: 4638 Sorted by residual: angle pdb=" C1D NDP A 501 " pdb=" O4D NDP A 501 " pdb=" C4D NDP A 501 " ideal model delta sigma weight residual 105.41 127.53 -22.12 2.71e+00 1.37e-01 6.68e+01 angle pdb=" C5B NDP A 501 " pdb=" O5B NDP A 501 " pdb=" PA NDP A 501 " ideal model delta sigma weight residual 103.84 119.24 -15.40 1.91e+00 2.73e-01 6.47e+01 angle pdb=" PA NDP A 501 " pdb=" O3 NDP A 501 " pdb=" PN NDP A 501 " ideal model delta sigma weight residual 107.74 122.52 -14.78 1.95e+00 2.62e-01 5.72e+01 angle pdb=" O1X NDP A 501 " pdb=" P2B NDP A 501 " pdb=" O3X NDP A 501 " ideal model delta sigma weight residual 117.46 109.42 8.04 1.17e+00 7.36e-01 4.75e+01 angle pdb=" O2X NDP A 501 " pdb=" P2B NDP A 501 " pdb=" O3X NDP A 501 " ideal model delta sigma weight residual 117.33 108.86 8.47 1.48e+00 4.57e-01 3.28e+01 ... (remaining 4633 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.95: 1931 30.95 - 61.89: 84 61.89 - 92.84: 7 92.84 - 123.78: 0 123.78 - 154.73: 1 Dihedral angle restraints: 2023 sinusoidal: 828 harmonic: 1195 Sorted by residual: dihedral pdb=" C5B NDP A 501 " pdb=" O5B NDP A 501 " pdb=" PA NDP A 501 " pdb=" O3 NDP A 501 " ideal model delta sinusoidal sigma weight residual 175.04 20.31 154.73 1 3.00e+01 1.11e-03 2.03e+01 dihedral pdb=" CA TYR A 101 " pdb=" C TYR A 101 " pdb=" N GLY A 102 " pdb=" CA GLY A 102 " ideal model delta harmonic sigma weight residual 180.00 163.83 16.17 0 5.00e+00 4.00e-02 1.05e+01 dihedral pdb=" CB LYS A 304 " pdb=" CG LYS A 304 " pdb=" CD LYS A 304 " pdb=" CE LYS A 304 " ideal model delta sinusoidal sigma weight residual 180.00 121.19 58.81 3 1.50e+01 4.44e-03 9.47e+00 ... (remaining 2020 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 443 0.079 - 0.159: 52 0.159 - 0.238: 3 0.238 - 0.318: 3 0.318 - 0.397: 3 Chirality restraints: 504 Sorted by residual: chirality pdb=" C4D NDP A 501 " pdb=" C3D NDP A 501 " pdb=" C5D NDP A 501 " pdb=" O4D NDP A 501 " both_signs ideal model delta sigma weight residual False -2.71 -2.32 -0.40 2.00e-01 2.50e+01 3.95e+00 chirality pdb=" C2D NDP A 501 " pdb=" C1D NDP A 501 " pdb=" C3D NDP A 501 " pdb=" O2D NDP A 501 " both_signs ideal model delta sigma weight residual False -2.71 -2.34 -0.37 2.00e-01 2.50e+01 3.42e+00 chirality pdb=" C1B NDP A 501 " pdb=" C2B NDP A 501 " pdb=" N9A NDP A 501 " pdb=" O4B NDP A 501 " both_signs ideal model delta sigma weight residual False 2.59 2.24 0.36 2.00e-01 2.50e+01 3.16e+00 ... (remaining 501 not shown) Planarity restraints: 592 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2N NDP A 501 " -0.139 2.00e-02 2.50e+03 8.17e-02 8.34e+01 pdb=" C3N NDP A 501 " 0.008 2.00e-02 2.50e+03 pdb=" C4N NDP A 501 " -0.026 2.00e-02 2.50e+03 pdb=" C7N NDP A 501 " 0.058 2.00e-02 2.50e+03 pdb=" N1N NDP A 501 " 0.100 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C4N NDP A 501 " -0.035 2.00e-02 2.50e+03 6.15e-02 3.78e+01 pdb=" C5N NDP A 501 " 0.078 2.00e-02 2.50e+03 pdb=" C6N NDP A 501 " -0.080 2.00e-02 2.50e+03 pdb=" N1N NDP A 501 " 0.038 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS A 394 " 0.021 2.00e-02 2.50e+03 4.08e-02 1.66e+01 pdb=" C HIS A 394 " -0.071 2.00e-02 2.50e+03 pdb=" O HIS A 394 " 0.026 2.00e-02 2.50e+03 pdb=" N MET A 395 " 0.024 2.00e-02 2.50e+03 ... (remaining 589 not shown) Histogram of nonbonded interaction distances: 2.38 - 2.88: 1265 2.88 - 3.39: 3295 3.39 - 3.89: 6079 3.89 - 4.40: 7212 4.40 - 4.90: 11655 Nonbonded interactions: 29506 Sorted by model distance: nonbonded pdb=" O HIS A 61 " pdb=" O HOH A 601 " model vdw 2.381 3.040 nonbonded pdb=" O ASP A 145 " pdb=" O HOH A 602 " model vdw 2.445 3.040 nonbonded pdb=" O VAL A 317 " pdb=" ND2 ASN A 344 " model vdw 2.448 3.120 nonbonded pdb=" O ARG A 65 " pdb=" O HOH A 603 " model vdw 2.461 3.040 nonbonded pdb=" O THR A 148 " pdb=" O HOH A 602 " model vdw 2.469 3.040 ... (remaining 29501 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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: 1.090 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: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.640 Find NCS groups from input model: 0.010 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:6.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 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 : 0.009 0.267 3415 Z= 0.350 Angle : 1.096 22.116 4638 Z= 0.584 Chirality : 0.059 0.397 504 Planarity : 0.006 0.082 592 Dihedral : 16.414 154.727 1261 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 4.69 % Allowed : 3.52 % Favored : 91.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.58 (0.43), residues: 416 helix: 0.93 (0.36), residues: 210 sheet: 0.54 (0.74), residues: 60 loop : -0.33 (0.56), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 129 TYR 0.007 0.001 TYR A 363 PHE 0.008 0.001 PHE A 341 TRP 0.006 0.001 TRP A 63 HIS 0.003 0.001 HIS A 388 Details of bonding type rmsd covalent geometry : bond 0.00887 ( 3415) covalent geometry : angle 1.09606 ( 4638) hydrogen bonds : bond 0.14336 ( 184) hydrogen bonds : angle 6.24967 ( 570) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 65 time to evaluate : 0.151 Fit side-chains REVERT: A 12 LYS cc_start: 0.8340 (OUTLIER) cc_final: 0.8073 (mptt) outliers start: 16 outliers final: 2 residues processed: 76 average time/residue: 0.8241 time to fit residues: 63.9149 Evaluate side-chains 50 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 47 time to evaluate : 0.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LYS Chi-restraints excluded: chain A residue 19 GLN Chi-restraints excluded: chain A residue 388 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 24 optimal weight: 0.9990 chunk 26 optimal weight: 0.9990 chunk 2 optimal weight: 3.9990 chunk 16 optimal weight: 4.9990 chunk 32 optimal weight: 3.9990 chunk 31 optimal weight: 0.9980 chunk 25 optimal weight: 7.9990 chunk 19 optimal weight: 1.9990 chunk 30 optimal weight: 5.9990 chunk 22 optimal weight: 2.9990 chunk 37 optimal weight: 6.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 GLN A 337 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.108479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2823 r_free = 0.2823 target = 0.082421 restraints weight = 4257.780| |-----------------------------------------------------------------------------| r_work (start): 0.2802 rms_B_bonded: 1.52 r_work: 0.2700 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.2592 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.2592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8993 moved from start: 0.1953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3415 Z= 0.137 Angle : 0.497 4.661 4638 Z= 0.264 Chirality : 0.043 0.131 504 Planarity : 0.005 0.043 592 Dihedral : 10.647 156.869 477 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 3.52 % Allowed : 10.26 % Favored : 86.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.35 (0.44), residues: 416 helix: 1.84 (0.36), residues: 211 sheet: 0.45 (0.72), residues: 61 loop : -0.25 (0.57), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 16 TYR 0.011 0.001 TYR A 408 PHE 0.012 0.001 PHE A 341 TRP 0.011 0.001 TRP A 364 HIS 0.005 0.001 HIS A 388 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 3415) covalent geometry : angle 0.49684 ( 4638) hydrogen bonds : bond 0.04290 ( 184) hydrogen bonds : angle 4.50547 ( 570) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 49 time to evaluate : 0.170 Fit side-chains REVERT: A 16 ARG cc_start: 0.8390 (ttm170) cc_final: 0.8179 (ttm170) REVERT: A 113 LYS cc_start: 0.8956 (mttp) cc_final: 0.8457 (mtpt) REVERT: A 229 LYS cc_start: 0.8849 (OUTLIER) cc_final: 0.8594 (tttp) REVERT: A 303 GLU cc_start: 0.7684 (OUTLIER) cc_final: 0.7415 (pt0) REVERT: A 340 ASP cc_start: 0.8491 (p0) cc_final: 0.8278 (p0) REVERT: A 368 GLU cc_start: 0.7725 (mt-10) cc_final: 0.7491 (mt-10) REVERT: A 371 GLU cc_start: 0.8018 (OUTLIER) cc_final: 0.7673 (pt0) outliers start: 12 outliers final: 2 residues processed: 56 average time/residue: 0.8429 time to fit residues: 48.2271 Evaluate side-chains 50 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 45 time to evaluate : 0.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 LYS Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 303 GLU Chi-restraints excluded: chain A residue 371 GLU Chi-restraints excluded: chain A residue 388 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 19 optimal weight: 5.9990 chunk 35 optimal weight: 1.9990 chunk 26 optimal weight: 7.9990 chunk 30 optimal weight: 10.0000 chunk 23 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 5 optimal weight: 6.9990 chunk 40 optimal weight: 0.9990 chunk 32 optimal weight: 0.9990 chunk 1 optimal weight: 5.9990 chunk 37 optimal weight: 0.9980 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 337 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.108545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2824 r_free = 0.2824 target = 0.082677 restraints weight = 4304.777| |-----------------------------------------------------------------------------| r_work (start): 0.2813 rms_B_bonded: 1.54 r_work: 0.2716 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2612 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.2612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8979 moved from start: 0.2187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3415 Z= 0.113 Angle : 0.463 5.253 4638 Z= 0.242 Chirality : 0.041 0.131 504 Planarity : 0.004 0.044 592 Dihedral : 9.115 151.739 470 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.05 % Allowed : 13.20 % Favored : 84.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.68 (0.44), residues: 416 helix: 2.13 (0.36), residues: 211 sheet: 0.47 (0.72), residues: 61 loop : -0.07 (0.59), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 16 TYR 0.009 0.001 TYR A 363 PHE 0.010 0.001 PHE A 341 TRP 0.006 0.001 TRP A 364 HIS 0.003 0.001 HIS A 388 Details of bonding type rmsd covalent geometry : bond 0.00251 ( 3415) covalent geometry : angle 0.46348 ( 4638) hydrogen bonds : bond 0.03920 ( 184) hydrogen bonds : angle 4.25061 ( 570) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 47 time to evaluate : 0.172 Fit side-chains REVERT: A 368 GLU cc_start: 0.7687 (mt-10) cc_final: 0.7424 (mt-10) REVERT: A 371 GLU cc_start: 0.8028 (pt0) cc_final: 0.7694 (pt0) outliers start: 7 outliers final: 1 residues processed: 52 average time/residue: 0.8350 time to fit residues: 44.4173 Evaluate side-chains 46 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 45 time to evaluate : 0.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 388 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 29 optimal weight: 8.9990 chunk 23 optimal weight: 8.9990 chunk 14 optimal weight: 1.9990 chunk 39 optimal weight: 0.1980 chunk 37 optimal weight: 1.9990 chunk 2 optimal weight: 4.9990 chunk 6 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 12 optimal weight: 8.9990 chunk 19 optimal weight: 5.9990 chunk 18 optimal weight: 4.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 337 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.107627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2805 r_free = 0.2805 target = 0.081666 restraints weight = 4213.340| |-----------------------------------------------------------------------------| r_work (start): 0.2802 rms_B_bonded: 1.51 r_work: 0.2702 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2596 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.2596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9000 moved from start: 0.2394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3415 Z= 0.118 Angle : 0.463 4.861 4638 Z= 0.244 Chirality : 0.042 0.129 504 Planarity : 0.004 0.043 592 Dihedral : 8.662 136.504 470 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.93 % Allowed : 13.49 % Favored : 83.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.75 (0.44), residues: 416 helix: 2.19 (0.36), residues: 211 sheet: 0.55 (0.73), residues: 61 loop : -0.06 (0.60), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 16 TYR 0.010 0.001 TYR A 363 PHE 0.012 0.001 PHE A 341 TRP 0.009 0.001 TRP A 30 HIS 0.004 0.001 HIS A 388 Details of bonding type rmsd covalent geometry : bond 0.00263 ( 3415) covalent geometry : angle 0.46345 ( 4638) hydrogen bonds : bond 0.04043 ( 184) hydrogen bonds : angle 4.23554 ( 570) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 47 time to evaluate : 0.147 Fit side-chains REVERT: A 4 ILE cc_start: 0.8198 (tp) cc_final: 0.7923 (tt) REVERT: A 78 GLU cc_start: 0.8638 (OUTLIER) cc_final: 0.8375 (tt0) REVERT: A 246 ARG cc_start: 0.8124 (OUTLIER) cc_final: 0.7632 (mtt180) REVERT: A 371 GLU cc_start: 0.8066 (pt0) cc_final: 0.7760 (pt0) REVERT: A 388 HIS cc_start: 0.8995 (OUTLIER) cc_final: 0.7981 (t70) outliers start: 10 outliers final: 2 residues processed: 51 average time/residue: 0.9109 time to fit residues: 47.4050 Evaluate side-chains 48 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 43 time to evaluate : 0.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 GLU Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 246 ARG Chi-restraints excluded: chain A residue 388 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 25 optimal weight: 9.9990 chunk 22 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 3 optimal weight: 10.0000 chunk 39 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 29 optimal weight: 9.9990 chunk 18 optimal weight: 6.9990 chunk 30 optimal weight: 4.9990 chunk 20 optimal weight: 20.0000 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 337 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.104319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2762 r_free = 0.2762 target = 0.078792 restraints weight = 4274.204| |-----------------------------------------------------------------------------| r_work (start): 0.2729 rms_B_bonded: 1.45 r_work: 0.2632 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.2529 rms_B_bonded: 3.02 restraints_weight: 0.2500 r_work (final): 0.2529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9026 moved from start: 0.2551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3415 Z= 0.173 Angle : 0.506 5.209 4638 Z= 0.268 Chirality : 0.044 0.135 504 Planarity : 0.004 0.045 592 Dihedral : 8.555 119.958 470 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 3.23 % Allowed : 12.32 % Favored : 84.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.58 (0.44), residues: 416 helix: 2.09 (0.36), residues: 211 sheet: 0.43 (0.73), residues: 61 loop : -0.18 (0.59), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 118 TYR 0.013 0.001 TYR A 363 PHE 0.019 0.002 PHE A 341 TRP 0.010 0.001 TRP A 364 HIS 0.007 0.002 HIS A 388 Details of bonding type rmsd covalent geometry : bond 0.00405 ( 3415) covalent geometry : angle 0.50639 ( 4638) hydrogen bonds : bond 0.04729 ( 184) hydrogen bonds : angle 4.44889 ( 570) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 43 time to evaluate : 0.135 Fit side-chains REVERT: A 4 ILE cc_start: 0.8204 (tp) cc_final: 0.7892 (tt) REVERT: A 78 GLU cc_start: 0.8737 (OUTLIER) cc_final: 0.8393 (tt0) REVERT: A 167 LYS cc_start: 0.9049 (mmtt) cc_final: 0.8700 (mmpt) REVERT: A 246 ARG cc_start: 0.8108 (OUTLIER) cc_final: 0.7526 (mtt180) REVERT: A 371 GLU cc_start: 0.8048 (OUTLIER) cc_final: 0.7721 (pt0) outliers start: 11 outliers final: 2 residues processed: 50 average time/residue: 0.9238 time to fit residues: 47.1493 Evaluate side-chains 48 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 43 time to evaluate : 0.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 GLU Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 246 ARG Chi-restraints excluded: chain A residue 371 GLU Chi-restraints excluded: chain A residue 388 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 0 optimal weight: 10.0000 chunk 37 optimal weight: 6.9990 chunk 10 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 chunk 18 optimal weight: 0.7980 chunk 13 optimal weight: 4.9990 chunk 36 optimal weight: 4.9990 chunk 38 optimal weight: 4.9990 chunk 2 optimal weight: 1.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 337 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.105052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2771 r_free = 0.2771 target = 0.079418 restraints weight = 4299.091| |-----------------------------------------------------------------------------| r_work (start): 0.2706 rms_B_bonded: 1.47 r_work: 0.2608 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.2504 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.2504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9011 moved from start: 0.2604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3415 Z= 0.158 Angle : 0.484 4.490 4638 Z= 0.257 Chirality : 0.043 0.138 504 Planarity : 0.004 0.047 592 Dihedral : 7.752 98.823 470 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 3.23 % Allowed : 12.32 % Favored : 84.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.55 (0.44), residues: 416 helix: 2.07 (0.35), residues: 211 sheet: 0.38 (0.72), residues: 61 loop : -0.20 (0.59), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 118 TYR 0.013 0.001 TYR A 363 PHE 0.016 0.002 PHE A 341 TRP 0.008 0.001 TRP A 30 HIS 0.006 0.001 HIS A 388 Details of bonding type rmsd covalent geometry : bond 0.00368 ( 3415) covalent geometry : angle 0.48356 ( 4638) hydrogen bonds : bond 0.04545 ( 184) hydrogen bonds : angle 4.41245 ( 570) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 45 time to evaluate : 0.138 Fit side-chains REVERT: A 4 ILE cc_start: 0.8179 (tp) cc_final: 0.7839 (tt) REVERT: A 78 GLU cc_start: 0.8730 (OUTLIER) cc_final: 0.8411 (tt0) REVERT: A 167 LYS cc_start: 0.9051 (mmtt) cc_final: 0.8667 (mmpt) REVERT: A 229 LYS cc_start: 0.8821 (OUTLIER) cc_final: 0.8522 (tttp) REVERT: A 230 LEU cc_start: 0.9085 (OUTLIER) cc_final: 0.8773 (mp) REVERT: A 246 ARG cc_start: 0.8061 (OUTLIER) cc_final: 0.7466 (mtt180) REVERT: A 371 GLU cc_start: 0.8023 (OUTLIER) cc_final: 0.7692 (pt0) REVERT: A 388 HIS cc_start: 0.9079 (OUTLIER) cc_final: 0.7884 (t70) outliers start: 11 outliers final: 1 residues processed: 52 average time/residue: 0.8772 time to fit residues: 46.5483 Evaluate side-chains 50 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 43 time to evaluate : 0.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 GLU Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 229 LYS Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 246 ARG Chi-restraints excluded: chain A residue 371 GLU Chi-restraints excluded: chain A residue 388 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 2 optimal weight: 0.3980 chunk 14 optimal weight: 1.9990 chunk 34 optimal weight: 8.9990 chunk 15 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 23 optimal weight: 6.9990 chunk 5 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 337 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.107053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2809 r_free = 0.2809 target = 0.081581 restraints weight = 4389.804| |-----------------------------------------------------------------------------| r_work (start): 0.2756 rms_B_bonded: 1.49 r_work: 0.2660 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.2557 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.2557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8989 moved from start: 0.2589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3415 Z= 0.115 Angle : 0.468 5.463 4638 Z= 0.246 Chirality : 0.042 0.134 504 Planarity : 0.004 0.046 592 Dihedral : 7.369 97.944 470 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.35 % Allowed : 14.08 % Favored : 83.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.69 (0.44), residues: 416 helix: 2.19 (0.36), residues: 211 sheet: 0.39 (0.72), residues: 61 loop : -0.11 (0.59), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 396 TYR 0.009 0.001 TYR A 363 PHE 0.011 0.001 PHE A 341 TRP 0.007 0.001 TRP A 382 HIS 0.004 0.001 HIS A 388 Details of bonding type rmsd covalent geometry : bond 0.00257 ( 3415) covalent geometry : angle 0.46809 ( 4638) hydrogen bonds : bond 0.03975 ( 184) hydrogen bonds : angle 4.21944 ( 570) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 47 time to evaluate : 0.134 Fit side-chains REVERT: A 4 ILE cc_start: 0.8126 (tp) cc_final: 0.7780 (tt) REVERT: A 78 GLU cc_start: 0.8671 (OUTLIER) cc_final: 0.8409 (tt0) REVERT: A 246 ARG cc_start: 0.8079 (OUTLIER) cc_final: 0.7496 (mtt180) REVERT: A 371 GLU cc_start: 0.8023 (OUTLIER) cc_final: 0.7711 (pt0) REVERT: A 388 HIS cc_start: 0.8899 (OUTLIER) cc_final: 0.8044 (t70) outliers start: 8 outliers final: 1 residues processed: 51 average time/residue: 0.8626 time to fit residues: 44.8892 Evaluate side-chains 49 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 44 time to evaluate : 0.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 GLU Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 246 ARG Chi-restraints excluded: chain A residue 371 GLU Chi-restraints excluded: chain A residue 388 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 9 optimal weight: 0.7980 chunk 36 optimal weight: 5.9990 chunk 17 optimal weight: 5.9990 chunk 10 optimal weight: 3.9990 chunk 21 optimal weight: 6.9990 chunk 15 optimal weight: 0.8980 chunk 28 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 6 optimal weight: 0.9980 chunk 18 optimal weight: 0.9980 chunk 1 optimal weight: 7.9990 overall best weight: 1.5382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 337 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.106623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2798 r_free = 0.2798 target = 0.080959 restraints weight = 4409.584| |-----------------------------------------------------------------------------| r_work (start): 0.2787 rms_B_bonded: 1.50 r_work: 0.2690 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.2587 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.2587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9011 moved from start: 0.2609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3415 Z= 0.127 Angle : 0.482 4.810 4638 Z= 0.252 Chirality : 0.042 0.133 504 Planarity : 0.004 0.046 592 Dihedral : 7.318 96.527 470 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.05 % Allowed : 13.78 % Favored : 84.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.69 (0.44), residues: 416 helix: 2.19 (0.36), residues: 211 sheet: 0.43 (0.73), residues: 61 loop : -0.13 (0.59), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 396 TYR 0.011 0.001 TYR A 363 PHE 0.013 0.001 PHE A 341 TRP 0.007 0.001 TRP A 382 HIS 0.005 0.001 HIS A 388 Details of bonding type rmsd covalent geometry : bond 0.00287 ( 3415) covalent geometry : angle 0.48197 ( 4638) hydrogen bonds : bond 0.04114 ( 184) hydrogen bonds : angle 4.25278 ( 570) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 45 time to evaluate : 0.084 Fit side-chains REVERT: A 4 ILE cc_start: 0.8122 (tp) cc_final: 0.7780 (tt) REVERT: A 78 GLU cc_start: 0.8646 (OUTLIER) cc_final: 0.8396 (tt0) REVERT: A 246 ARG cc_start: 0.8104 (OUTLIER) cc_final: 0.7518 (mtt180) REVERT: A 371 GLU cc_start: 0.8066 (OUTLIER) cc_final: 0.7754 (pt0) REVERT: A 388 HIS cc_start: 0.8973 (OUTLIER) cc_final: 0.8006 (t70) outliers start: 7 outliers final: 1 residues processed: 48 average time/residue: 0.8654 time to fit residues: 42.4092 Evaluate side-chains 50 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 45 time to evaluate : 0.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 GLU Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 246 ARG Chi-restraints excluded: chain A residue 371 GLU Chi-restraints excluded: chain A residue 388 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 16 optimal weight: 1.9990 chunk 34 optimal weight: 4.9990 chunk 27 optimal weight: 4.9990 chunk 7 optimal weight: 4.9990 chunk 31 optimal weight: 10.0000 chunk 4 optimal weight: 0.1980 chunk 6 optimal weight: 0.7980 chunk 26 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 23 optimal weight: 6.9990 chunk 29 optimal weight: 0.0770 overall best weight: 0.7740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 337 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.109534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.084051 restraints weight = 4352.688| |-----------------------------------------------------------------------------| r_work (start): 0.2796 rms_B_bonded: 1.49 r_work: 0.2700 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.2598 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.2598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8951 moved from start: 0.2630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 3415 Z= 0.099 Angle : 0.454 4.860 4638 Z= 0.236 Chirality : 0.041 0.129 504 Planarity : 0.004 0.046 592 Dihedral : 7.003 93.268 470 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.76 % Allowed : 14.37 % Favored : 83.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.81 (0.44), residues: 416 helix: 2.29 (0.36), residues: 211 sheet: 0.45 (0.73), residues: 61 loop : -0.06 (0.59), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 396 TYR 0.007 0.001 TYR A 363 PHE 0.008 0.001 PHE A 341 TRP 0.007 0.001 TRP A 63 HIS 0.002 0.001 HIS A 388 Details of bonding type rmsd covalent geometry : bond 0.00215 ( 3415) covalent geometry : angle 0.45438 ( 4638) hydrogen bonds : bond 0.03575 ( 184) hydrogen bonds : angle 4.05427 ( 570) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 49 time to evaluate : 0.085 Fit side-chains REVERT: A 4 ILE cc_start: 0.8019 (tp) cc_final: 0.7686 (tt) REVERT: A 246 ARG cc_start: 0.8066 (OUTLIER) cc_final: 0.7404 (mtt180) REVERT: A 368 GLU cc_start: 0.7704 (mt-10) cc_final: 0.7417 (mt-10) REVERT: A 371 GLU cc_start: 0.8002 (OUTLIER) cc_final: 0.7700 (pt0) REVERT: A 388 HIS cc_start: 0.8666 (OUTLIER) cc_final: 0.8280 (t70) outliers start: 6 outliers final: 1 residues processed: 51 average time/residue: 0.8872 time to fit residues: 46.1372 Evaluate side-chains 50 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 46 time to evaluate : 0.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 246 ARG Chi-restraints excluded: chain A residue 371 GLU Chi-restraints excluded: chain A residue 388 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 18 optimal weight: 7.9990 chunk 15 optimal weight: 5.9990 chunk 24 optimal weight: 20.0000 chunk 35 optimal weight: 0.9990 chunk 31 optimal weight: 10.0000 chunk 28 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 19 optimal weight: 1.9990 chunk 38 optimal weight: 7.9990 chunk 17 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 337 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.104127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2763 r_free = 0.2763 target = 0.078908 restraints weight = 4326.648| |-----------------------------------------------------------------------------| r_work (start): 0.2759 rms_B_bonded: 1.42 r_work: 0.2664 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.2563 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.2563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9064 moved from start: 0.2678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 3415 Z= 0.209 Angle : 0.536 5.353 4638 Z= 0.282 Chirality : 0.046 0.140 504 Planarity : 0.005 0.047 592 Dihedral : 7.609 95.682 470 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.76 % Allowed : 14.37 % Favored : 83.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.55 (0.44), residues: 416 helix: 2.19 (0.35), residues: 206 sheet: 0.40 (0.73), residues: 61 loop : -0.33 (0.57), residues: 149 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 118 TYR 0.015 0.002 TYR A 363 PHE 0.022 0.002 PHE A 341 TRP 0.010 0.002 TRP A 364 HIS 0.008 0.002 HIS A 388 Details of bonding type rmsd covalent geometry : bond 0.00496 ( 3415) covalent geometry : angle 0.53641 ( 4638) hydrogen bonds : bond 0.04961 ( 184) hydrogen bonds : angle 4.50567 ( 570) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 43 time to evaluate : 0.160 Fit side-chains REVERT: A 4 ILE cc_start: 0.8306 (tp) cc_final: 0.7973 (tt) REVERT: A 78 GLU cc_start: 0.8714 (tt0) cc_final: 0.8377 (tt0) REVERT: A 167 LYS cc_start: 0.9085 (mmtt) cc_final: 0.8718 (mmpt) REVERT: A 246 ARG cc_start: 0.8186 (OUTLIER) cc_final: 0.7559 (mtt180) REVERT: A 371 GLU cc_start: 0.8190 (OUTLIER) cc_final: 0.7879 (pt0) outliers start: 6 outliers final: 2 residues processed: 46 average time/residue: 0.9330 time to fit residues: 43.7928 Evaluate side-chains 46 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 42 time to evaluate : 0.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 246 ARG Chi-restraints excluded: chain A residue 371 GLU Chi-restraints excluded: chain A residue 388 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 27 optimal weight: 10.0000 chunk 9 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 19 optimal weight: 5.9990 chunk 21 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 20 optimal weight: 5.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 337 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.104530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2759 r_free = 0.2759 target = 0.078762 restraints weight = 4449.938| |-----------------------------------------------------------------------------| r_work (start): 0.2700 rms_B_bonded: 1.49 r_work: 0.2603 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.2498 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.2498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9018 moved from start: 0.2682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3415 Z= 0.162 Angle : 0.508 5.302 4638 Z= 0.267 Chirality : 0.044 0.135 504 Planarity : 0.004 0.047 592 Dihedral : 7.498 96.726 470 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.47 % Allowed : 14.66 % Favored : 83.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.54 (0.44), residues: 416 helix: 2.20 (0.36), residues: 206 sheet: 0.39 (0.72), residues: 61 loop : -0.35 (0.56), residues: 149 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 118 TYR 0.013 0.001 TYR A 363 PHE 0.017 0.002 PHE A 341 TRP 0.008 0.001 TRP A 263 HIS 0.006 0.001 HIS A 388 Details of bonding type rmsd covalent geometry : bond 0.00380 ( 3415) covalent geometry : angle 0.50821 ( 4638) hydrogen bonds : bond 0.04570 ( 184) hydrogen bonds : angle 4.42531 ( 570) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1565.29 seconds wall clock time: 27 minutes 29.96 seconds (1649.96 seconds total)