Starting phenix.real_space_refine on Fri Aug 22 13:49:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qt9_18646/08_2025/8qt9_18646.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qt9_18646/08_2025/8qt9_18646.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8qt9_18646/08_2025/8qt9_18646.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qt9_18646/08_2025/8qt9_18646.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8qt9_18646/08_2025/8qt9_18646.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qt9_18646/08_2025/8qt9_18646.map" } resolution = 2.36 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= 0.074 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 Fe 2 7.16 5 P 4 5.49 5 S 11 5.16 5 C 2282 2.51 5 N 555 2.21 5 O 657 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3511 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 3264 Classifications: {'peptide': 399} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 385} Chain: "A" Number of atoms: 247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 247 Unusual residues: {'FAD': 1, 'HEM': 2, 'NAI': 1} Classifications: {'undetermined': 4, 'water': 64} Link IDs: {None: 67} Time building chain proxies: 0.95, per 1000 atoms: 0.27 Number of scatterers: 3511 At special positions: 0 Unit cell: (63.985, 61.12, 92.635, 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) Fe 2 26.01 S 11 16.00 P 4 15.00 O 657 8.00 N 555 7.00 C 2282 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.26 Conformation dependent library (CDL) restraints added in 121.6 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 740 Finding SS restraints... Secondary structure from input PDB file: 16 helices and 2 sheets defined 55.6% alpha, 20.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.12 Creating SS restraints... Processing helix chain 'A' and resid 4 through 6 No H-bonds generated for 'chain 'A' and resid 4 through 6' Processing helix chain 'A' and resid 7 through 29 Processing helix chain 'A' and resid 32 through 48 removed outlier: 3.559A pdb=" N THR A 45 " --> pdb=" O SER A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 60 Processing helix chain 'A' and resid 61 through 88 Processing helix chain 'A' and resid 94 through 117 removed outlier: 3.589A pdb=" N GLY A 100 " --> pdb=" O ALA A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 130 Processing helix chain 'A' and resid 131 through 148 Processing helix chain 'A' and resid 155 through 178 Processing helix chain 'A' and resid 178 through 183 Processing helix chain 'A' and resid 253 through 263 removed outlier: 3.596A pdb=" N LEU A 263 " --> pdb=" O ILE A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 283 Processing helix chain 'A' and resid 296 through 306 removed outlier: 3.554A pdb=" N SER A 301 " --> pdb=" O THR A 297 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N TYR A 302 " --> pdb=" O PRO A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 325 Processing helix chain 'A' and resid 327 through 338 Processing helix chain 'A' and resid 372 through 387 Processing sheet with id=AA1, first strand: chain 'A' and resid 186 through 195 removed outlier: 8.035A pdb=" N TYR A 186 " --> pdb=" O PRO A 210 " (cutoff:3.500A) removed outlier: 8.392A pdb=" N GLY A 188 " --> pdb=" O SER A 208 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N SER A 208 " --> pdb=" O GLY A 188 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N ILE A 190 " --> pdb=" O HIS A 206 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N HIS A 206 " --> pdb=" O ILE A 190 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N HIS A 192 " --> pdb=" O GLN A 204 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N GLN A 243 " --> pdb=" O LEU A 207 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N TYR A 246 " --> pdb=" O SER A 238 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N THR A 248 " --> pdb=" O SER A 236 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N SER A 236 " --> pdb=" O THR A 248 " (cutoff:3.500A) removed outlier: 8.829A pdb=" N LYS A 250 " --> pdb=" O PRO A 234 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N PHE A 220 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N ARG A 273 " --> pdb=" O PHE A 220 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N LYS A 222 " --> pdb=" O LEU A 271 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N LEU A 271 " --> pdb=" O LYS A 222 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N PHE A 224 " --> pdb=" O VAL A 269 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N VAL A 269 " --> pdb=" O PHE A 224 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 341 through 347 removed outlier: 6.550A pdb=" N VAL A 313 " --> pdb=" O GLU A 342 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N HIS A 344 " --> pdb=" O VAL A 313 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N PHE A 315 " --> pdb=" O HIS A 344 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N ILE A 346 " --> pdb=" O PHE A 315 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N TYR A 317 " --> pdb=" O ILE A 346 " (cutoff:3.500A) 193 hydrogen bonds defined for protein. 555 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: 0.52 Time building geometry restraints manager: 0.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.38: 1429 1.38 - 1.56: 2100 1.56 - 1.73: 8 1.73 - 1.90: 21 1.90 - 2.07: 8 Bond restraints: 3566 Sorted by residual: bond pdb=" O5B FAD A 501 " pdb=" PA FAD A 501 " ideal model delta sigma weight residual 1.634 1.558 0.076 2.00e-02 2.50e+03 1.45e+01 bond pdb=" O5B NAI A 504 " pdb=" PA NAI A 504 " ideal model delta sigma weight residual 1.644 1.571 0.073 2.00e-02 2.50e+03 1.32e+01 bond pdb=" O3P FAD A 501 " pdb=" P FAD A 501 " ideal model delta sigma weight residual 1.660 1.593 0.067 2.00e-02 2.50e+03 1.14e+01 bond pdb=" O5D NAI A 504 " pdb=" PN NAI A 504 " ideal model delta sigma weight residual 1.650 1.583 0.067 2.00e-02 2.50e+03 1.12e+01 bond pdb=" O5' FAD A 501 " pdb=" P FAD A 501 " ideal model delta sigma weight residual 1.637 1.570 0.067 2.00e-02 2.50e+03 1.11e+01 ... (remaining 3561 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.89: 4764 1.89 - 3.78: 80 3.78 - 5.66: 22 5.66 - 7.55: 6 7.55 - 9.44: 2 Bond angle restraints: 4874 Sorted by residual: angle pdb=" O1N NAI A 504 " pdb=" PN NAI A 504 " pdb=" O2N NAI A 504 " ideal model delta sigma weight residual 123.22 113.78 9.44 3.00e+00 1.11e-01 9.90e+00 angle pdb=" PA NAI A 504 " pdb=" O3 NAI A 504 " pdb=" PN NAI A 504 " ideal model delta sigma weight residual 129.27 136.82 -7.55 3.00e+00 1.11e-01 6.34e+00 angle pdb=" C GLU A 229 " pdb=" CA GLU A 229 " pdb=" CB GLU A 229 " ideal model delta sigma weight residual 109.53 113.77 -4.24 1.69e+00 3.50e-01 6.28e+00 angle pdb=" O1P FAD A 501 " pdb=" P FAD A 501 " pdb=" O2P FAD A 501 " ideal model delta sigma weight residual 122.50 115.08 7.42 3.00e+00 1.11e-01 6.12e+00 angle pdb=" C MET A 87 " pdb=" N GLY A 88 " pdb=" CA GLY A 88 " ideal model delta sigma weight residual 121.83 118.94 2.89 1.19e+00 7.06e-01 5.90e+00 ... (remaining 4869 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.78: 1724 17.78 - 35.56: 226 35.56 - 53.34: 65 53.34 - 71.13: 33 71.13 - 88.91: 15 Dihedral angle restraints: 2063 sinusoidal: 901 harmonic: 1162 Sorted by residual: dihedral pdb=" CA ASP A 261 " pdb=" CB ASP A 261 " pdb=" CG ASP A 261 " pdb=" OD1 ASP A 261 " ideal model delta sinusoidal sigma weight residual -30.00 -90.26 60.26 1 2.00e+01 2.50e-03 1.21e+01 dihedral pdb=" C1A HEM A 503 " pdb=" C2A HEM A 503 " pdb=" CAA HEM A 503 " pdb=" CBA HEM A 503 " ideal model delta sinusoidal sigma weight residual -180.00 -101.61 -78.39 2 2.00e+01 2.50e-03 1.15e+01 dihedral pdb=" CA ASP A 261 " pdb=" C ASP A 261 " pdb=" N ASN A 262 " pdb=" CA ASN A 262 " ideal model delta harmonic sigma weight residual -180.00 -163.31 -16.69 0 5.00e+00 4.00e-02 1.11e+01 ... (remaining 2060 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 301 0.029 - 0.058: 126 0.058 - 0.086: 42 0.086 - 0.115: 28 0.115 - 0.144: 12 Chirality restraints: 509 Sorted by residual: chirality pdb=" CA THR A 297 " pdb=" N THR A 297 " pdb=" C THR A 297 " pdb=" CB THR A 297 " both_signs ideal model delta sigma weight residual False 2.53 2.38 0.14 2.00e-01 2.50e+01 5.18e-01 chirality pdb=" C1D NAI A 504 " pdb=" C2D NAI A 504 " pdb=" N1N NAI A 504 " pdb=" O4D NAI A 504 " both_signs ideal model delta sigma weight residual False 2.29 2.43 -0.14 2.00e-01 2.50e+01 4.76e-01 chirality pdb=" C2B FAD A 501 " pdb=" C1B FAD A 501 " pdb=" C3B FAD A 501 " pdb=" O2B FAD A 501 " both_signs ideal model delta sigma weight residual False -2.53 -2.66 0.13 2.00e-01 2.50e+01 4.10e-01 ... (remaining 506 not shown) Planarity restraints: 579 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR A 40 " -0.006 2.00e-02 2.50e+03 1.19e-02 1.41e+00 pdb=" C THR A 40 " 0.021 2.00e-02 2.50e+03 pdb=" O THR A 40 " -0.008 2.00e-02 2.50e+03 pdb=" N SER A 41 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN A 338 " -0.018 5.00e-02 4.00e+02 2.74e-02 1.20e+00 pdb=" N PRO A 339 " 0.047 5.00e-02 4.00e+02 pdb=" CA PRO A 339 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 339 " -0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR A 45 " 0.005 2.00e-02 2.50e+03 1.06e-02 1.13e+00 pdb=" C THR A 45 " -0.018 2.00e-02 2.50e+03 pdb=" O THR A 45 " 0.007 2.00e-02 2.50e+03 pdb=" N PHE A 46 " 0.006 2.00e-02 2.50e+03 ... (remaining 576 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 121 2.71 - 3.26: 3290 3.26 - 3.80: 6330 3.80 - 4.35: 8359 4.35 - 4.90: 13188 Nonbonded interactions: 31288 Sorted by model distance: nonbonded pdb=" NE2 HIS A 69 " pdb="FE HEM A 502 " model vdw 2.158 3.080 nonbonded pdb=" O HOH A 601 " pdb=" O HOH A 636 " model vdw 2.197 3.040 nonbonded pdb=" O1P FAD A 501 " pdb=" O HOH A 601 " model vdw 2.203 3.040 nonbonded pdb=" O2A FAD A 501 " pdb=" O HOH A 601 " model vdw 2.211 3.040 nonbonded pdb=" O SER A 236 " pdb=" O HOH A 602 " model vdw 2.218 3.040 ... (remaining 31283 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: 2.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.010 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:5.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 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 : 0.005 0.076 3568 Z= 0.250 Angle : 0.685 9.439 4874 Z= 0.314 Chirality : 0.043 0.144 509 Planarity : 0.003 0.027 579 Dihedral : 20.317 88.907 1323 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 0.58 % Allowed : 22.19 % Favored : 77.23 % 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 (0.41), residues: 397 helix: 1.14 (0.36), residues: 204 sheet: 0.08 (0.52), residues: 88 loop : -0.67 (0.58), residues: 105 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 51 TYR 0.013 0.001 TYR A 144 PHE 0.008 0.001 PHE A 32 TRP 0.003 0.001 TRP A 25 HIS 0.006 0.001 HIS A 69 Details of bonding type rmsd covalent geometry : bond 0.00521 ( 3566) covalent geometry : angle 0.68489 ( 4874) hydrogen bonds : bond 0.13953 ( 193) hydrogen bonds : angle 7.13357 ( 555) Misc. bond : bond 0.05061 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 45 time to evaluate : 0.140 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 47 average time/residue: 0.5482 time to fit residues: 26.5572 Evaluate side-chains 47 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 45 time to evaluate : 0.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 GLU Chi-restraints excluded: chain A residue 93 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 24 optimal weight: 0.9990 chunk 26 optimal weight: 0.3980 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 31 optimal weight: 0.5980 chunk 25 optimal weight: 0.7980 chunk 19 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 37 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.131512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.114647 restraints weight = 3347.892| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 1.26 r_work: 0.3205 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.3102 rms_B_bonded: 2.82 restraints_weight: 0.2500 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.0774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.160 3568 Z= 0.138 Angle : 0.646 13.786 4874 Z= 0.278 Chirality : 0.041 0.139 509 Planarity : 0.003 0.027 579 Dihedral : 12.306 85.915 564 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 2.59 % Allowed : 19.02 % Favored : 78.39 % 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: 1.59 (0.42), residues: 397 helix: 2.02 (0.35), residues: 204 sheet: 0.25 (0.56), residues: 82 loop : -0.02 (0.63), residues: 111 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 195 TYR 0.014 0.001 TYR A 144 PHE 0.007 0.001 PHE A 32 TRP 0.012 0.001 TRP A 25 HIS 0.004 0.001 HIS A 69 Details of bonding type rmsd covalent geometry : bond 0.00310 ( 3566) covalent geometry : angle 0.64616 ( 4874) hydrogen bonds : bond 0.04175 ( 193) hydrogen bonds : angle 4.79555 ( 555) Misc. bond : bond 0.15242 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 50 time to evaluate : 0.171 Fit side-chains REVERT: A 78 ILE cc_start: 0.8190 (OUTLIER) cc_final: 0.7773 (mp) outliers start: 9 outliers final: 4 residues processed: 54 average time/residue: 0.4388 time to fit residues: 24.5832 Evaluate side-chains 52 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 47 time to evaluate : 0.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 312 GLN Chi-restraints excluded: chain A residue 392 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 24 optimal weight: 0.0030 chunk 35 optimal weight: 0.8980 chunk 8 optimal weight: 0.0870 chunk 34 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 9 optimal weight: 0.7980 chunk 2 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 overall best weight: 0.5570 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.132171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.115342 restraints weight = 3339.280| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 1.27 r_work: 0.3212 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.3112 rms_B_bonded: 2.82 restraints_weight: 0.2500 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.0909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.147 3568 Z= 0.124 Angle : 0.609 12.855 4874 Z= 0.263 Chirality : 0.040 0.136 509 Planarity : 0.003 0.026 579 Dihedral : 11.545 88.607 560 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.59 % Allowed : 19.60 % Favored : 77.81 % 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 (0.42), residues: 397 helix: 2.18 (0.35), residues: 204 sheet: 0.23 (0.56), residues: 82 loop : -0.12 (0.60), residues: 111 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 195 TYR 0.014 0.001 TYR A 144 PHE 0.007 0.001 PHE A 218 TRP 0.008 0.001 TRP A 25 HIS 0.004 0.001 HIS A 69 Details of bonding type rmsd covalent geometry : bond 0.00285 ( 3566) covalent geometry : angle 0.60868 ( 4874) hydrogen bonds : bond 0.03900 ( 193) hydrogen bonds : angle 4.60422 ( 555) Misc. bond : bond 0.13812 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 48 time to evaluate : 0.105 Fit side-chains REVERT: A 78 ILE cc_start: 0.8169 (OUTLIER) cc_final: 0.7756 (mp) REVERT: A 268 LYS cc_start: 0.8326 (OUTLIER) cc_final: 0.7674 (mttp) outliers start: 9 outliers final: 3 residues processed: 53 average time/residue: 0.4920 time to fit residues: 26.8880 Evaluate side-chains 53 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 48 time to evaluate : 0.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 268 LYS Chi-restraints excluded: chain A residue 312 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 21 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 6 optimal weight: 0.8980 chunk 20 optimal weight: 3.9990 chunk 24 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 8 optimal weight: 6.9990 chunk 35 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 ASN ** A 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 241 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.130084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.113190 restraints weight = 3293.592| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 1.26 r_work: 0.3187 rms_B_bonded: 1.64 restraints_weight: 0.5000 r_work: 0.3085 rms_B_bonded: 2.78 restraints_weight: 0.2500 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.0906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.150 3568 Z= 0.164 Angle : 0.656 12.804 4874 Z= 0.289 Chirality : 0.042 0.136 509 Planarity : 0.003 0.028 579 Dihedral : 12.054 85.345 560 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.88 % Allowed : 19.02 % Favored : 78.10 % 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: 1.48 (0.41), residues: 397 helix: 2.01 (0.35), residues: 204 sheet: 0.16 (0.56), residues: 82 loop : -0.23 (0.59), residues: 111 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 195 TYR 0.017 0.002 TYR A 144 PHE 0.010 0.001 PHE A 224 TRP 0.007 0.001 TRP A 25 HIS 0.006 0.001 HIS A 69 Details of bonding type rmsd covalent geometry : bond 0.00380 ( 3566) covalent geometry : angle 0.65611 ( 4874) hydrogen bonds : bond 0.04435 ( 193) hydrogen bonds : angle 4.74330 ( 555) Misc. bond : bond 0.14563 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 48 time to evaluate : 0.114 Fit side-chains REVERT: A 78 ILE cc_start: 0.8193 (OUTLIER) cc_final: 0.7771 (mp) REVERT: A 268 LYS cc_start: 0.8361 (OUTLIER) cc_final: 0.7695 (mttp) outliers start: 10 outliers final: 7 residues processed: 53 average time/residue: 0.4428 time to fit residues: 24.2646 Evaluate side-chains 56 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 47 time to evaluate : 0.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 121 GLN Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 268 LYS Chi-restraints excluded: chain A residue 312 GLN Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 392 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 6 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 4 optimal weight: 0.7980 chunk 34 optimal weight: 0.7980 chunk 15 optimal weight: 0.9990 chunk 9 optimal weight: 0.3980 chunk 27 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 16 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 ASN ** A 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 241 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.130979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.114018 restraints weight = 3347.052| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 1.27 r_work: 0.3195 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.3093 rms_B_bonded: 2.81 restraints_weight: 0.2500 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.0933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.144 3568 Z= 0.143 Angle : 0.630 12.731 4874 Z= 0.277 Chirality : 0.041 0.135 509 Planarity : 0.003 0.028 579 Dihedral : 11.842 86.042 560 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.59 % Allowed : 19.88 % Favored : 77.52 % 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: 1.50 (0.41), residues: 397 helix: 2.05 (0.35), residues: 204 sheet: 0.17 (0.56), residues: 82 loop : -0.26 (0.58), residues: 111 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 195 TYR 0.015 0.002 TYR A 144 PHE 0.008 0.001 PHE A 224 TRP 0.007 0.001 TRP A 25 HIS 0.005 0.001 HIS A 69 Details of bonding type rmsd covalent geometry : bond 0.00330 ( 3566) covalent geometry : angle 0.63012 ( 4874) hydrogen bonds : bond 0.04132 ( 193) hydrogen bonds : angle 4.68523 ( 555) Misc. bond : bond 0.14172 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 46 time to evaluate : 0.136 Fit side-chains REVERT: A 78 ILE cc_start: 0.8208 (OUTLIER) cc_final: 0.7785 (mp) REVERT: A 268 LYS cc_start: 0.8354 (OUTLIER) cc_final: 0.7688 (mttp) outliers start: 9 outliers final: 6 residues processed: 50 average time/residue: 0.4808 time to fit residues: 24.7986 Evaluate side-chains 54 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 46 time to evaluate : 0.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 121 GLN Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 268 LYS Chi-restraints excluded: chain A residue 312 GLN Chi-restraints excluded: chain A residue 392 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 19 optimal weight: 2.9990 chunk 35 optimal weight: 0.8980 chunk 23 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 37 optimal weight: 0.6980 chunk 0 optimal weight: 5.9990 chunk 1 optimal weight: 0.9990 chunk 4 optimal weight: 0.6980 chunk 38 optimal weight: 0.9990 chunk 17 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 ASN ** A 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 241 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.130449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.113494 restraints weight = 3326.021| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 1.26 r_work: 0.3190 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.3087 rms_B_bonded: 2.81 restraints_weight: 0.2500 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.0977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.143 3568 Z= 0.154 Angle : 0.641 12.637 4874 Z= 0.283 Chirality : 0.042 0.136 509 Planarity : 0.003 0.028 579 Dihedral : 11.998 85.905 560 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.59 % Allowed : 19.31 % Favored : 78.10 % 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: 1.45 (0.41), residues: 397 helix: 2.03 (0.35), residues: 204 sheet: 0.17 (0.56), residues: 82 loop : -0.35 (0.57), residues: 111 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 51 TYR 0.016 0.002 TYR A 144 PHE 0.008 0.001 PHE A 224 TRP 0.007 0.001 TRP A 25 HIS 0.005 0.001 HIS A 69 Details of bonding type rmsd covalent geometry : bond 0.00356 ( 3566) covalent geometry : angle 0.64147 ( 4874) hydrogen bonds : bond 0.04283 ( 193) hydrogen bonds : angle 4.71101 ( 555) Misc. bond : bond 0.14141 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 47 time to evaluate : 0.139 Fit side-chains REVERT: A 78 ILE cc_start: 0.8177 (OUTLIER) cc_final: 0.7759 (mp) REVERT: A 268 LYS cc_start: 0.8358 (OUTLIER) cc_final: 0.7685 (mttp) outliers start: 9 outliers final: 7 residues processed: 51 average time/residue: 0.5189 time to fit residues: 27.3710 Evaluate side-chains 56 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 47 time to evaluate : 0.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 121 GLN Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 268 LYS Chi-restraints excluded: chain A residue 312 GLN Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 392 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 21 optimal weight: 0.9980 chunk 7 optimal weight: 0.8980 chunk 15 optimal weight: 0.2980 chunk 4 optimal weight: 0.9990 chunk 13 optimal weight: 0.6980 chunk 23 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 8 optimal weight: 0.0970 chunk 11 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 30 optimal weight: 3.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 ASN A 241 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.131954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.114995 restraints weight = 3369.367| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 1.27 r_work: 0.3210 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.3107 rms_B_bonded: 2.83 restraints_weight: 0.2500 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.1019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.148 3568 Z= 0.128 Angle : 0.608 12.770 4874 Z= 0.264 Chirality : 0.041 0.135 509 Planarity : 0.003 0.028 579 Dihedral : 11.750 88.423 560 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.59 % Allowed : 20.17 % Favored : 77.23 % 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 (0.41), residues: 397 helix: 2.15 (0.34), residues: 204 sheet: 0.18 (0.56), residues: 82 loop : -0.37 (0.57), residues: 111 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 195 TYR 0.014 0.002 TYR A 144 PHE 0.007 0.001 PHE A 218 TRP 0.007 0.001 TRP A 25 HIS 0.004 0.001 HIS A 69 Details of bonding type rmsd covalent geometry : bond 0.00294 ( 3566) covalent geometry : angle 0.60829 ( 4874) hydrogen bonds : bond 0.03881 ( 193) hydrogen bonds : angle 4.59641 ( 555) Misc. bond : bond 0.13770 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 49 time to evaluate : 0.106 Fit side-chains REVERT: A 78 ILE cc_start: 0.8160 (OUTLIER) cc_final: 0.7743 (mp) REVERT: A 268 LYS cc_start: 0.8333 (OUTLIER) cc_final: 0.7677 (mttp) outliers start: 9 outliers final: 6 residues processed: 53 average time/residue: 0.4610 time to fit residues: 25.2356 Evaluate side-chains 56 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 48 time to evaluate : 0.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 121 GLN Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 268 LYS Chi-restraints excluded: chain A residue 312 GLN Chi-restraints excluded: chain A residue 392 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 36 optimal weight: 1.9990 chunk 3 optimal weight: 0.5980 chunk 2 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 33 optimal weight: 0.1980 chunk 15 optimal weight: 0.8980 chunk 7 optimal weight: 0.5980 chunk 24 optimal weight: 0.4980 chunk 25 optimal weight: 0.9980 chunk 0 optimal weight: 5.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.132116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.115223 restraints weight = 3372.304| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 1.27 r_work: 0.3214 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.3112 rms_B_bonded: 2.82 restraints_weight: 0.2500 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.1009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.145 3568 Z= 0.124 Angle : 0.605 12.733 4874 Z= 0.263 Chirality : 0.041 0.134 509 Planarity : 0.003 0.028 579 Dihedral : 11.740 89.085 560 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.88 % Allowed : 20.75 % Favored : 76.37 % 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: 1.57 (0.41), residues: 397 helix: 2.18 (0.34), residues: 204 sheet: 0.17 (0.56), residues: 82 loop : -0.37 (0.58), residues: 111 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 126 TYR 0.014 0.001 TYR A 144 PHE 0.007 0.001 PHE A 218 TRP 0.008 0.001 TRP A 25 HIS 0.004 0.001 HIS A 69 Details of bonding type rmsd covalent geometry : bond 0.00285 ( 3566) covalent geometry : angle 0.60509 ( 4874) hydrogen bonds : bond 0.03830 ( 193) hydrogen bonds : angle 4.57713 ( 555) Misc. bond : bond 0.13415 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 46 time to evaluate : 0.117 Fit side-chains REVERT: A 78 ILE cc_start: 0.8167 (OUTLIER) cc_final: 0.7744 (mp) REVERT: A 241 HIS cc_start: 0.7518 (p-80) cc_final: 0.7283 (p90) REVERT: A 268 LYS cc_start: 0.8342 (OUTLIER) cc_final: 0.7660 (mttp) outliers start: 10 outliers final: 7 residues processed: 52 average time/residue: 0.4659 time to fit residues: 25.0404 Evaluate side-chains 55 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 46 time to evaluate : 0.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 121 GLN Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 268 LYS Chi-restraints excluded: chain A residue 312 GLN Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 392 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 9 optimal weight: 0.6980 chunk 18 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 4 optimal weight: 0.4980 chunk 33 optimal weight: 0.3980 chunk 15 optimal weight: 0.0980 chunk 3 optimal weight: 0.6980 chunk 20 optimal weight: 7.9990 chunk 34 optimal weight: 0.5980 chunk 6 optimal weight: 0.8980 chunk 16 optimal weight: 0.8980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.133501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.116643 restraints weight = 3279.695| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 1.26 r_work: 0.3231 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.3129 rms_B_bonded: 2.82 restraints_weight: 0.2500 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.1108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.138 3568 Z= 0.113 Angle : 0.585 12.344 4874 Z= 0.254 Chirality : 0.040 0.134 509 Planarity : 0.003 0.028 579 Dihedral : 11.574 88.715 560 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.31 % Allowed : 21.33 % Favored : 76.37 % 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: 1.64 (0.42), residues: 397 helix: 2.26 (0.35), residues: 204 sheet: 0.17 (0.56), residues: 82 loop : -0.36 (0.58), residues: 111 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 195 TYR 0.013 0.001 TYR A 144 PHE 0.007 0.001 PHE A 218 TRP 0.008 0.001 TRP A 25 HIS 0.004 0.001 HIS A 69 Details of bonding type rmsd covalent geometry : bond 0.00261 ( 3566) covalent geometry : angle 0.58521 ( 4874) hydrogen bonds : bond 0.03593 ( 193) hydrogen bonds : angle 4.48623 ( 555) Misc. bond : bond 0.12521 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 48 time to evaluate : 0.136 Fit side-chains REVERT: A 78 ILE cc_start: 0.8122 (OUTLIER) cc_final: 0.7715 (mp) REVERT: A 241 HIS cc_start: 0.7615 (p-80) cc_final: 0.7394 (p90) REVERT: A 268 LYS cc_start: 0.8299 (OUTLIER) cc_final: 0.7653 (mttp) outliers start: 8 outliers final: 4 residues processed: 52 average time/residue: 0.4600 time to fit residues: 24.7054 Evaluate side-chains 54 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 48 time to evaluate : 0.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 268 LYS Chi-restraints excluded: chain A residue 312 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 17 optimal weight: 2.9990 chunk 32 optimal weight: 0.5980 chunk 20 optimal weight: 0.9980 chunk 18 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 33 optimal weight: 0.2980 chunk 16 optimal weight: 0.6980 chunk 6 optimal weight: 0.7980 chunk 7 optimal weight: 0.6980 chunk 2 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.132157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.115134 restraints weight = 3352.242| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 1.28 r_work: 0.3212 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.3108 rms_B_bonded: 2.85 restraints_weight: 0.2500 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.1050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.139 3568 Z= 0.130 Angle : 0.614 12.822 4874 Z= 0.268 Chirality : 0.041 0.134 509 Planarity : 0.003 0.029 579 Dihedral : 11.800 89.558 560 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.73 % Allowed : 22.19 % Favored : 76.08 % 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 (0.41), residues: 397 helix: 2.18 (0.34), residues: 204 sheet: 0.14 (0.56), residues: 82 loop : -0.33 (0.58), residues: 111 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 195 TYR 0.015 0.001 TYR A 144 PHE 0.007 0.001 PHE A 224 TRP 0.007 0.001 TRP A 25 HIS 0.004 0.001 HIS A 69 Details of bonding type rmsd covalent geometry : bond 0.00300 ( 3566) covalent geometry : angle 0.61380 ( 4874) hydrogen bonds : bond 0.03902 ( 193) hydrogen bonds : angle 4.56957 ( 555) Misc. bond : bond 0.13058 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 47 time to evaluate : 0.087 Fit side-chains REVERT: A 78 ILE cc_start: 0.8149 (OUTLIER) cc_final: 0.7733 (mp) REVERT: A 241 HIS cc_start: 0.7621 (p-80) cc_final: 0.7381 (p90) REVERT: A 268 LYS cc_start: 0.8354 (OUTLIER) cc_final: 0.7680 (mttp) outliers start: 6 outliers final: 4 residues processed: 51 average time/residue: 0.5280 time to fit residues: 27.7634 Evaluate side-chains 53 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 47 time to evaluate : 0.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 268 LYS Chi-restraints excluded: chain A residue 312 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 5 optimal weight: 0.9990 chunk 34 optimal weight: 0.7980 chunk 11 optimal weight: 3.9990 chunk 32 optimal weight: 0.5980 chunk 37 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 chunk 10 optimal weight: 1.9990 chunk 1 optimal weight: 0.5980 chunk 24 optimal weight: 0.2980 chunk 19 optimal weight: 0.5980 chunk 36 optimal weight: 0.4980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.132914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.116008 restraints weight = 3309.442| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 1.26 r_work: 0.3223 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.3121 rms_B_bonded: 2.81 restraints_weight: 0.2500 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.1109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.139 3568 Z= 0.120 Angle : 0.598 12.514 4874 Z= 0.260 Chirality : 0.041 0.134 509 Planarity : 0.003 0.028 579 Dihedral : 11.683 89.947 560 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 2.31 % Allowed : 21.90 % Favored : 75.79 % 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: 1.62 (0.41), residues: 397 helix: 2.23 (0.34), residues: 204 sheet: 0.15 (0.56), residues: 82 loop : -0.33 (0.58), residues: 111 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 195 TYR 0.014 0.001 TYR A 144 PHE 0.007 0.001 PHE A 218 TRP 0.007 0.001 TRP A 25 HIS 0.004 0.001 HIS A 69 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 3566) covalent geometry : angle 0.59794 ( 4874) hydrogen bonds : bond 0.03726 ( 193) hydrogen bonds : angle 4.51558 ( 555) Misc. bond : bond 0.12868 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1350.29 seconds wall clock time: 23 minutes 43.97 seconds (1423.97 seconds total)