Starting phenix.real_space_refine on Fri Aug 22 13:20:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dwi_27755/08_2025/8dwi_27755.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dwi_27755/08_2025/8dwi_27755.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8dwi_27755/08_2025/8dwi_27755.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dwi_27755/08_2025/8dwi_27755.map" model { file = "/net/cci-nas-00/data/ceres_data/8dwi_27755/08_2025/8dwi_27755.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dwi_27755/08_2025/8dwi_27755.cif" } resolution = 3.4 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= 0.002 sd= 0.018 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: 4 Type Number sf(0) Gaussians S 14 5.16 5 C 2138 2.51 5 N 504 2.21 5 O 536 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: 3192 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 424, 3192 Classifications: {'peptide': 424} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 19, 'TRANS': 404} Chain breaks: 1 Unresolved non-hydrogen bonds: 118 Unresolved non-hydrogen angles: 150 Unresolved non-hydrogen dihedrals: 92 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'ASP:plan': 4, 'TYR:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 4, 'GLN:plan1': 3, 'GLU:plan': 4} Unresolved non-hydrogen planarities: 71 Time building chain proxies: 1.19, per 1000 atoms: 0.37 Number of scatterers: 3192 At special positions: 0 Unit cell: (71.38, 70.55, 72.21, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 14 16.00 O 536 8.00 N 504 7.00 C 2138 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: 0.27 Conformation dependent library (CDL) restraints added in 131.7 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 772 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 0 sheets defined 76.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.06 Creating SS restraints... Processing helix chain 'A' and resid 38 through 67 removed outlier: 4.163A pdb=" N PHE A 47 " --> pdb=" O ILE A 44 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N PHE A 48 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N TYR A 54 " --> pdb=" O PHE A 51 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N ASN A 59 " --> pdb=" O LEU A 56 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N LEU A 60 " --> pdb=" O ARG A 57 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N SER A 61 " --> pdb=" O VAL A 58 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N LEU A 64 " --> pdb=" O SER A 61 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N MET A 67 " --> pdb=" O LEU A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 133 removed outlier: 4.773A pdb=" N PHE A 115 " --> pdb=" O ILE A 111 " (cutoff:3.500A) removed outlier: 5.525A pdb=" N PHE A 116 " --> pdb=" O LEU A 112 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N TYR A 117 " --> pdb=" O GLY A 113 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLY A 118 " --> pdb=" O SER A 114 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N ILE A 121 " --> pdb=" O TYR A 117 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N ILE A 124 " --> pdb=" O ILE A 120 " (cutoff:3.500A) Proline residue: A 125 - end of helix removed outlier: 4.502A pdb=" N TYR A 128 " --> pdb=" O ILE A 124 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LYS A 132 " --> pdb=" O TYR A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 151 Processing helix chain 'A' and resid 153 through 159 Processing helix chain 'A' and resid 161 through 168 Processing helix chain 'A' and resid 176 through 189 Proline residue: A 180 - end of helix removed outlier: 3.910A pdb=" N SER A 188 " --> pdb=" O ALA A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 223 removed outlier: 3.849A pdb=" N GLY A 205 " --> pdb=" O ILE A 201 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N ALA A 206 " --> pdb=" O SER A 202 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N GLN A 207 " --> pdb=" O TYR A 203 " (cutoff:3.500A) Proline residue: A 215 - end of helix Processing helix chain 'A' and resid 226 through 247 removed outlier: 5.193A pdb=" N PHE A 233 " --> pdb=" O PHE A 230 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N TRP A 244 " --> pdb=" O PHE A 241 " (cutoff:3.500A) removed outlier: 5.257A pdb=" N ILE A 245 " --> pdb=" O LEU A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 272 Processing helix chain 'A' and resid 282 through 287 Processing helix chain 'A' and resid 289 through 310 Processing helix chain 'A' and resid 312 through 318 Processing helix chain 'A' and resid 324 through 354 removed outlier: 3.981A pdb=" N SER A 331 " --> pdb=" O ASN A 327 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N SER A 332 " --> pdb=" O GLY A 328 " (cutoff:3.500A) Proline residue: A 334 - end of helix removed outlier: 3.871A pdb=" N GLN A 347 " --> pdb=" O ILE A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 382 removed outlier: 4.217A pdb=" N GLY A 374 " --> pdb=" O ILE A 370 " (cutoff:3.500A) Proline residue: A 375 - end of helix Processing helix chain 'A' and resid 389 through 408 removed outlier: 3.960A pdb=" N PHE A 405 " --> pdb=" O THR A 401 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N CYS A 406 " --> pdb=" O LEU A 402 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N SER A 407 " --> pdb=" O GLY A 403 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N SER A 408 " --> pdb=" O GLY A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 417 removed outlier: 4.321A pdb=" N LEU A 415 " --> pdb=" O ILE A 412 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ILE A 417 " --> pdb=" O HIS A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 431 Processing helix chain 'A' and resid 435 through 445 Proline residue: A 441 - end of helix Processing helix chain 'A' and resid 453 through 477 Processing helix chain 'A' and resid 484 through 486 No H-bonds generated for 'chain 'A' and resid 484 through 486' 197 hydrogen bonds defined for protein. 480 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: 0.30 Time building geometry restraints manager: 0.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 938 1.34 - 1.46: 817 1.46 - 1.58: 1515 1.58 - 1.69: 0 1.69 - 1.81: 22 Bond restraints: 3292 Sorted by residual: bond pdb=" N TYR A 117 " pdb=" CA TYR A 117 " ideal model delta sigma weight residual 1.457 1.483 -0.025 1.29e-02 6.01e+03 3.89e+00 bond pdb=" N PHE A 115 " pdb=" CA PHE A 115 " ideal model delta sigma weight residual 1.458 1.481 -0.024 1.30e-02 5.92e+03 3.31e+00 bond pdb=" C VAL A 58 " pdb=" O VAL A 58 " ideal model delta sigma weight residual 1.242 1.230 0.012 1.13e-02 7.83e+03 1.22e+00 bond pdb=" C LEU A 214 " pdb=" N PRO A 215 " ideal model delta sigma weight residual 1.335 1.350 -0.015 1.36e-02 5.41e+03 1.18e+00 bond pdb=" C PHE A 115 " pdb=" N PHE A 116 " ideal model delta sigma weight residual 1.334 1.320 0.014 1.43e-02 4.89e+03 9.67e-01 ... (remaining 3287 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.28: 4313 1.28 - 2.56: 148 2.56 - 3.84: 28 3.84 - 5.12: 13 5.12 - 6.40: 5 Bond angle restraints: 4507 Sorted by residual: angle pdb=" N ILE A 435 " pdb=" CA ILE A 435 " pdb=" C ILE A 435 " ideal model delta sigma weight residual 112.61 107.45 5.16 1.45e+00 4.76e-01 1.27e+01 angle pdb=" N PHE A 115 " pdb=" CA PHE A 115 " pdb=" C PHE A 115 " ideal model delta sigma weight residual 112.38 108.50 3.88 1.22e+00 6.72e-01 1.01e+01 angle pdb=" C LYS A 256 " pdb=" N ARG A 257 " pdb=" CA ARG A 257 " ideal model delta sigma weight residual 121.54 127.49 -5.95 1.91e+00 2.74e-01 9.71e+00 angle pdb=" N PHE A 116 " pdb=" CA PHE A 116 " pdb=" C PHE A 116 " ideal model delta sigma weight residual 111.69 107.87 3.82 1.23e+00 6.61e-01 9.63e+00 angle pdb=" N VAL A 177 " pdb=" CA VAL A 177 " pdb=" C VAL A 177 " ideal model delta sigma weight residual 113.07 109.28 3.79 1.36e+00 5.41e-01 7.75e+00 ... (remaining 4502 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.49: 1648 15.49 - 30.97: 142 30.97 - 46.46: 43 46.46 - 61.95: 3 61.95 - 77.44: 2 Dihedral angle restraints: 1838 sinusoidal: 627 harmonic: 1211 Sorted by residual: dihedral pdb=" CA LEU A 170 " pdb=" C LEU A 170 " pdb=" N GLU A 171 " pdb=" CA GLU A 171 " ideal model delta harmonic sigma weight residual 180.00 160.10 19.90 0 5.00e+00 4.00e-02 1.58e+01 dihedral pdb=" CA LYS A 445 " pdb=" C LYS A 445 " pdb=" N SER A 446 " pdb=" CA SER A 446 " ideal model delta harmonic sigma weight residual 180.00 162.07 17.93 0 5.00e+00 4.00e-02 1.29e+01 dihedral pdb=" CA ALA A 382 " pdb=" C ALA A 382 " pdb=" N GLY A 383 " pdb=" CA GLY A 383 " ideal model delta harmonic sigma weight residual 180.00 162.09 17.91 0 5.00e+00 4.00e-02 1.28e+01 ... (remaining 1835 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 278 0.027 - 0.054: 148 0.054 - 0.082: 58 0.082 - 0.109: 32 0.109 - 0.136: 5 Chirality restraints: 521 Sorted by residual: chirality pdb=" CB VAL A 177 " pdb=" CA VAL A 177 " pdb=" CG1 VAL A 177 " pdb=" CG2 VAL A 177 " both_signs ideal model delta sigma weight residual False -2.63 -2.49 -0.14 2.00e-01 2.50e+01 4.62e-01 chirality pdb=" CA PHE A 115 " pdb=" N PHE A 115 " pdb=" C PHE A 115 " pdb=" CB PHE A 115 " both_signs ideal model delta sigma weight residual False 2.51 2.64 -0.13 2.00e-01 2.50e+01 4.24e-01 chirality pdb=" CA TRP A 186 " pdb=" N TRP A 186 " pdb=" C TRP A 186 " pdb=" CB TRP A 186 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.70e-01 ... (remaining 518 not shown) Planarity restraints: 547 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 435 " 0.050 5.00e-02 4.00e+02 7.51e-02 9.02e+00 pdb=" N PRO A 436 " -0.130 5.00e-02 4.00e+02 pdb=" CA PRO A 436 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 436 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 162 " -0.041 5.00e-02 4.00e+02 6.20e-02 6.15e+00 pdb=" N PRO A 163 " 0.107 5.00e-02 4.00e+02 pdb=" CA PRO A 163 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 163 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 374 " -0.037 5.00e-02 4.00e+02 5.66e-02 5.13e+00 pdb=" N PRO A 375 " 0.098 5.00e-02 4.00e+02 pdb=" CA PRO A 375 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 375 " -0.032 5.00e-02 4.00e+02 ... (remaining 544 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 816 2.79 - 3.32: 3337 3.32 - 3.84: 5401 3.84 - 4.37: 6043 4.37 - 4.90: 10257 Nonbonded interactions: 25854 Sorted by model distance: nonbonded pdb=" OG1 THR A 304 " pdb=" OD1 ASN A 467 " model vdw 2.258 3.040 nonbonded pdb=" N ASP A 104 " pdb=" OD1 ASP A 104 " model vdw 2.447 3.120 nonbonded pdb=" O ALA A 46 " pdb=" N PHE A 50 " model vdw 2.517 3.120 nonbonded pdb=" O PHE A 116 " pdb=" N GLY A 118 " model vdw 2.524 3.120 nonbonded pdb=" O ASN A 323 " pdb=" N ASN A 327 " model vdw 2.545 3.120 ... (remaining 25849 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: 2.450 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: 0.030 Process input model: 4.860 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 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:0.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3203 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 : 0.003 0.032 3292 Z= 0.162 Angle : 0.629 6.398 4507 Z= 0.365 Chirality : 0.042 0.136 521 Planarity : 0.006 0.075 547 Dihedral : 13.015 77.435 1066 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % 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: 0.29 (0.43), residues: 420 helix: 0.78 (0.30), residues: 327 sheet: None (None), residues: 0 loop : -1.77 (0.61), residues: 93 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 168 TYR 0.010 0.001 TYR A 335 PHE 0.016 0.001 PHE A 299 TRP 0.020 0.001 TRP A 246 HIS 0.007 0.001 HIS A 414 Details of bonding type rmsd covalent geometry : bond 0.00314 ( 3292) covalent geometry : angle 0.62851 ( 4507) hydrogen bonds : bond 0.07602 ( 197) hydrogen bonds : angle 4.63218 ( 480) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.117 Fit side-chains REVERT: A 230 PHE cc_start: 0.4985 (m-80) cc_final: 0.4557 (m-10) REVERT: A 244 TRP cc_start: 0.3185 (t60) cc_final: 0.2467 (t60) REVERT: A 247 LEU cc_start: 0.6669 (mt) cc_final: 0.6219 (pp) REVERT: A 342 MET cc_start: 0.5783 (ttm) cc_final: 0.5446 (mtm) REVERT: A 432 PHE cc_start: 0.3628 (m-80) cc_final: 0.2892 (m-10) outliers start: 0 outliers final: 0 residues processed: 56 average time/residue: 0.0730 time to fit residues: 5.0118 Evaluate side-chains 34 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 34 time to evaluate : 0.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 24 optimal weight: 0.5980 chunk 26 optimal weight: 0.7980 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 0.4980 chunk 32 optimal weight: 0.7980 chunk 31 optimal weight: 0.3980 chunk 25 optimal weight: 0.5980 chunk 19 optimal weight: 7.9990 chunk 30 optimal weight: 0.9990 chunk 22 optimal weight: 6.9990 chunk 37 optimal weight: 0.3980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 123 GLN A 207 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4535 r_free = 0.4535 target = 0.215209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.182207 restraints weight = 4556.439| |-----------------------------------------------------------------------------| r_work (start): 0.4231 rms_B_bonded: 3.91 r_work (final): 0.4231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3982 moved from start: 0.3491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3292 Z= 0.165 Angle : 0.682 7.251 4507 Z= 0.350 Chirality : 0.043 0.142 521 Planarity : 0.006 0.061 547 Dihedral : 4.945 17.813 448 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 2.23 % Allowed : 12.42 % Favored : 85.35 % 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: -0.29 (0.42), residues: 420 helix: 0.41 (0.29), residues: 323 sheet: None (None), residues: 0 loop : -2.05 (0.61), residues: 97 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 39 TYR 0.010 0.001 TYR A 421 PHE 0.029 0.002 PHE A 116 TRP 0.021 0.002 TRP A 103 HIS 0.007 0.003 HIS A 414 Details of bonding type rmsd covalent geometry : bond 0.00347 ( 3292) covalent geometry : angle 0.68197 ( 4507) hydrogen bonds : bond 0.04537 ( 197) hydrogen bonds : angle 4.49253 ( 480) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 42 time to evaluate : 0.108 Fit side-chains REVERT: A 244 TRP cc_start: 0.3457 (t60) cc_final: 0.2525 (t60) REVERT: A 247 LEU cc_start: 0.7048 (mt) cc_final: 0.6456 (pp) REVERT: A 316 MET cc_start: 0.6257 (mpp) cc_final: 0.5401 (mmm) outliers start: 7 outliers final: 3 residues processed: 45 average time/residue: 0.0572 time to fit residues: 3.2573 Evaluate side-chains 34 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 31 time to evaluate : 0.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 TYR Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 439 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 20 optimal weight: 3.9990 chunk 39 optimal weight: 0.4980 chunk 29 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 2 optimal weight: 0.6980 chunk 24 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4700 r_free = 0.4700 target = 0.218890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4378 r_free = 0.4378 target = 0.187201 restraints weight = 4572.210| |-----------------------------------------------------------------------------| r_work (start): 0.4373 rms_B_bonded: 3.07 r_work: 0.4233 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.4233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5755 moved from start: 0.7954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 3292 Z= 0.243 Angle : 0.801 8.586 4507 Z= 0.418 Chirality : 0.049 0.288 521 Planarity : 0.007 0.066 547 Dihedral : 5.357 26.328 448 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 4.14 % Allowed : 21.34 % Favored : 74.52 % 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: -1.57 (0.38), residues: 420 helix: -0.46 (0.28), residues: 315 sheet: None (None), residues: 0 loop : -2.54 (0.51), residues: 105 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.002 ARG A 39 TYR 0.013 0.002 TYR A 315 PHE 0.035 0.003 PHE A 115 TRP 0.020 0.002 TRP A 103 HIS 0.007 0.002 HIS A 183 Details of bonding type rmsd covalent geometry : bond 0.00541 ( 3292) covalent geometry : angle 0.80086 ( 4507) hydrogen bonds : bond 0.05636 ( 197) hydrogen bonds : angle 5.04247 ( 480) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 51 time to evaluate : 0.094 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 165 ILE cc_start: 0.8277 (tp) cc_final: 0.7996 (tp) REVERT: A 167 LEU cc_start: 0.7180 (OUTLIER) cc_final: 0.6946 (tp) REVERT: A 226 TRP cc_start: 0.6480 (p-90) cc_final: 0.5894 (p-90) REVERT: A 438 MET cc_start: 0.7344 (tmm) cc_final: 0.6950 (mtm) outliers start: 13 outliers final: 5 residues processed: 59 average time/residue: 0.0498 time to fit residues: 3.8803 Evaluate side-chains 44 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 38 time to evaluate : 0.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain A residue 473 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 10 optimal weight: 0.3980 chunk 20 optimal weight: 6.9990 chunk 13 optimal weight: 0.8980 chunk 26 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 chunk 15 optimal weight: 0.6980 chunk 17 optimal weight: 0.5980 chunk 33 optimal weight: 2.9990 chunk 23 optimal weight: 0.5980 chunk 25 optimal weight: 0.2980 chunk 4 optimal weight: 0.8980 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 183 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4782 r_free = 0.4782 target = 0.226611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4488 r_free = 0.4488 target = 0.194487 restraints weight = 4346.906| |-----------------------------------------------------------------------------| r_work (start): 0.4372 rms_B_bonded: 3.14 r_work: 0.4203 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.4203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5877 moved from start: 0.8907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 3292 Z= 0.149 Angle : 0.616 5.320 4507 Z= 0.323 Chirality : 0.042 0.137 521 Planarity : 0.006 0.056 547 Dihedral : 4.852 20.247 448 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 2.87 % Allowed : 23.25 % Favored : 73.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.73 (0.40), residues: 420 helix: 0.13 (0.29), residues: 312 sheet: None (None), residues: 0 loop : -2.10 (0.52), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 39 TYR 0.012 0.001 TYR A 203 PHE 0.017 0.002 PHE A 322 TRP 0.012 0.001 TRP A 240 HIS 0.007 0.002 HIS A 183 Details of bonding type rmsd covalent geometry : bond 0.00314 ( 3292) covalent geometry : angle 0.61556 ( 4507) hydrogen bonds : bond 0.04493 ( 197) hydrogen bonds : angle 4.65838 ( 480) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 43 time to evaluate : 0.125 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 165 ILE cc_start: 0.8442 (tp) cc_final: 0.8129 (tp) REVERT: A 167 LEU cc_start: 0.7534 (OUTLIER) cc_final: 0.7257 (tp) REVERT: A 226 TRP cc_start: 0.6144 (p-90) cc_final: 0.5769 (p-90) outliers start: 9 outliers final: 4 residues processed: 49 average time/residue: 0.0584 time to fit residues: 3.6843 Evaluate side-chains 42 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 37 time to evaluate : 0.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 432 PHE Chi-restraints excluded: chain A residue 473 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 33 optimal weight: 1.9990 chunk 20 optimal weight: 6.9990 chunk 38 optimal weight: 0.7980 chunk 14 optimal weight: 0.4980 chunk 32 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 16 optimal weight: 0.6980 chunk 1 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 39 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 HIS A 488 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4584 r_free = 0.4584 target = 0.200839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.166484 restraints weight = 4903.538| |-----------------------------------------------------------------------------| r_work (start): 0.4271 rms_B_bonded: 3.47 r_work: 0.4099 rms_B_bonded: 4.96 restraints_weight: 0.5000 r_work (final): 0.4099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6392 moved from start: 1.1136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 3292 Z= 0.184 Angle : 0.697 8.905 4507 Z= 0.358 Chirality : 0.045 0.139 521 Planarity : 0.006 0.061 547 Dihedral : 4.980 18.642 448 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 5.41 % Allowed : 23.25 % Favored : 71.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.69 (0.40), residues: 420 helix: 0.20 (0.30), residues: 306 sheet: None (None), residues: 0 loop : -2.10 (0.49), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.002 ARG A 364 TYR 0.009 0.001 TYR A 203 PHE 0.018 0.002 PHE A 322 TRP 0.013 0.002 TRP A 240 HIS 0.007 0.001 HIS A 414 Details of bonding type rmsd covalent geometry : bond 0.00400 ( 3292) covalent geometry : angle 0.69697 ( 4507) hydrogen bonds : bond 0.05054 ( 197) hydrogen bonds : angle 4.73015 ( 480) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 49 time to evaluate : 0.093 Fit side-chains revert: symmetry clash REVERT: A 167 LEU cc_start: 0.7440 (OUTLIER) cc_final: 0.7199 (tt) REVERT: A 185 MET cc_start: 0.6873 (tpp) cc_final: 0.6636 (tpp) REVERT: A 244 TRP cc_start: 0.6945 (OUTLIER) cc_final: 0.6615 (t-100) outliers start: 17 outliers final: 8 residues processed: 60 average time/residue: 0.0402 time to fit residues: 3.2694 Evaluate side-chains 49 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 39 time to evaluate : 0.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 103 TRP Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 244 TRP Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 473 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 29 optimal weight: 0.9990 chunk 37 optimal weight: 0.5980 chunk 19 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 11 optimal weight: 0.7980 chunk 13 optimal weight: 0.8980 chunk 35 optimal weight: 0.0670 chunk 22 optimal weight: 0.6980 chunk 25 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4565 r_free = 0.4565 target = 0.201345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.166953 restraints weight = 4584.904| |-----------------------------------------------------------------------------| r_work (start): 0.4202 rms_B_bonded: 3.09 r_work: 0.4070 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.4070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6442 moved from start: 1.1923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3292 Z= 0.149 Angle : 0.674 10.410 4507 Z= 0.330 Chirality : 0.043 0.181 521 Planarity : 0.006 0.062 547 Dihedral : 5.006 21.532 448 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 3.18 % Allowed : 27.71 % Favored : 69.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.36 (0.40), residues: 420 helix: 0.46 (0.30), residues: 303 sheet: None (None), residues: 0 loop : -1.98 (0.50), residues: 117 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 364 TYR 0.007 0.001 TYR A 306 PHE 0.012 0.001 PHE A 299 TRP 0.019 0.001 TRP A 240 HIS 0.008 0.001 HIS A 414 Details of bonding type rmsd covalent geometry : bond 0.00327 ( 3292) covalent geometry : angle 0.67441 ( 4507) hydrogen bonds : bond 0.04332 ( 197) hydrogen bonds : angle 4.60340 ( 480) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 43 time to evaluate : 0.140 Fit side-chains REVERT: A 165 ILE cc_start: 0.8617 (OUTLIER) cc_final: 0.8321 (tp) REVERT: A 167 LEU cc_start: 0.7602 (OUTLIER) cc_final: 0.7314 (tp) REVERT: A 185 MET cc_start: 0.7246 (tpp) cc_final: 0.7001 (tpp) REVERT: A 189 TRP cc_start: 0.7611 (OUTLIER) cc_final: 0.7215 (m100) outliers start: 10 outliers final: 3 residues processed: 51 average time/residue: 0.0558 time to fit residues: 3.7011 Evaluate side-chains 45 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 39 time to evaluate : 0.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 189 TRP Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 473 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 16 optimal weight: 0.7980 chunk 7 optimal weight: 0.5980 chunk 1 optimal weight: 0.2980 chunk 35 optimal weight: 2.9990 chunk 17 optimal weight: 0.3980 chunk 24 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 2 optimal weight: 0.8980 chunk 11 optimal weight: 0.5980 chunk 14 optimal weight: 0.8980 chunk 12 optimal weight: 0.4980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4547 r_free = 0.4547 target = 0.199777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.166482 restraints weight = 4585.996| |-----------------------------------------------------------------------------| r_work (start): 0.4193 rms_B_bonded: 3.19 r_work: 0.4051 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.4051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6578 moved from start: 1.2471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 3292 Z= 0.147 Angle : 0.682 9.919 4507 Z= 0.328 Chirality : 0.043 0.165 521 Planarity : 0.006 0.063 547 Dihedral : 4.822 19.999 448 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 4.14 % Allowed : 28.03 % Favored : 67.83 % 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: -0.26 (0.41), residues: 420 helix: 0.52 (0.30), residues: 303 sheet: None (None), residues: 0 loop : -1.92 (0.50), residues: 117 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 364 TYR 0.005 0.001 TYR A 389 PHE 0.019 0.001 PHE A 115 TRP 0.013 0.001 TRP A 240 HIS 0.008 0.001 HIS A 414 Details of bonding type rmsd covalent geometry : bond 0.00327 ( 3292) covalent geometry : angle 0.68177 ( 4507) hydrogen bonds : bond 0.04330 ( 197) hydrogen bonds : angle 4.52804 ( 480) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 46 time to evaluate : 0.123 Fit side-chains revert: symmetry clash REVERT: A 167 LEU cc_start: 0.7625 (OUTLIER) cc_final: 0.7346 (tp) REVERT: A 185 MET cc_start: 0.7432 (tpp) cc_final: 0.7117 (tpp) outliers start: 13 outliers final: 4 residues processed: 55 average time/residue: 0.0551 time to fit residues: 3.8092 Evaluate side-chains 44 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 39 time to evaluate : 0.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 TRP Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 189 TRP Chi-restraints excluded: chain A residue 373 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 32 optimal weight: 4.9990 chunk 41 optimal weight: 0.0270 chunk 4 optimal weight: 0.4980 chunk 22 optimal weight: 0.0670 chunk 16 optimal weight: 0.7980 chunk 7 optimal weight: 2.9990 chunk 10 optimal weight: 0.2980 chunk 19 optimal weight: 0.0470 chunk 15 optimal weight: 0.0770 chunk 39 optimal weight: 2.9990 chunk 2 optimal weight: 0.5980 overall best weight: 0.1032 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4693 r_free = 0.4693 target = 0.218790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4370 r_free = 0.4370 target = 0.183435 restraints weight = 4597.192| |-----------------------------------------------------------------------------| r_work (start): 0.4525 rms_B_bonded: 3.48 r_work: 0.4404 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.4404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6305 moved from start: 1.2643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3292 Z= 0.126 Angle : 0.651 8.054 4507 Z= 0.311 Chirality : 0.041 0.191 521 Planarity : 0.006 0.057 547 Dihedral : 4.746 18.655 448 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 3.18 % Allowed : 28.98 % Favored : 67.83 % 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: -0.09 (0.41), residues: 420 helix: 0.68 (0.31), residues: 307 sheet: None (None), residues: 0 loop : -2.04 (0.50), residues: 113 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 57 TYR 0.008 0.001 TYR A 128 PHE 0.012 0.001 PHE A 299 TRP 0.010 0.001 TRP A 226 HIS 0.006 0.001 HIS A 414 Details of bonding type rmsd covalent geometry : bond 0.00252 ( 3292) covalent geometry : angle 0.65134 ( 4507) hydrogen bonds : bond 0.04122 ( 197) hydrogen bonds : angle 4.33163 ( 480) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 46 time to evaluate : 0.073 Fit side-chains revert: symmetry clash REVERT: A 128 TYR cc_start: 0.7973 (t80) cc_final: 0.6763 (m-10) REVERT: A 137 MET cc_start: 0.6865 (mpp) cc_final: 0.6595 (mmt) REVERT: A 167 LEU cc_start: 0.7184 (OUTLIER) cc_final: 0.6930 (tp) REVERT: A 185 MET cc_start: 0.7405 (tpp) cc_final: 0.6995 (tpp) REVERT: A 189 TRP cc_start: 0.7750 (OUTLIER) cc_final: 0.7263 (m100) outliers start: 10 outliers final: 6 residues processed: 53 average time/residue: 0.0359 time to fit residues: 2.5351 Evaluate side-chains 52 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 44 time to evaluate : 0.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 103 TRP Chi-restraints excluded: chain A residue 110 TRP Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 189 TRP Chi-restraints excluded: chain A residue 373 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 0.9990 chunk 17 optimal weight: 0.3980 chunk 37 optimal weight: 0.9990 chunk 30 optimal weight: 0.8980 chunk 4 optimal weight: 0.9980 chunk 3 optimal weight: 0.0060 chunk 39 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 40 optimal weight: 0.6980 chunk 11 optimal weight: 0.6980 chunk 26 optimal weight: 0.9980 overall best weight: 0.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4540 r_free = 0.4540 target = 0.199060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.163864 restraints weight = 4657.877| |-----------------------------------------------------------------------------| r_work (start): 0.4399 rms_B_bonded: 3.23 r_work: 0.4283 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.4283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6552 moved from start: 1.3337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3292 Z= 0.140 Angle : 0.657 8.341 4507 Z= 0.318 Chirality : 0.042 0.194 521 Planarity : 0.006 0.057 547 Dihedral : 4.685 18.341 448 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 2.87 % Allowed : 29.30 % Favored : 67.83 % 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: -0.23 (0.41), residues: 420 helix: 0.56 (0.30), residues: 311 sheet: None (None), residues: 0 loop : -2.13 (0.52), residues: 109 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 39 TYR 0.007 0.001 TYR A 389 PHE 0.013 0.001 PHE A 47 TRP 0.010 0.001 TRP A 240 HIS 0.006 0.001 HIS A 414 Details of bonding type rmsd covalent geometry : bond 0.00297 ( 3292) covalent geometry : angle 0.65675 ( 4507) hydrogen bonds : bond 0.04320 ( 197) hydrogen bonds : angle 4.42477 ( 480) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 49 time to evaluate : 0.083 Fit side-chains REVERT: A 128 TYR cc_start: 0.8030 (t80) cc_final: 0.6884 (m-10) REVERT: A 137 MET cc_start: 0.6977 (mpp) cc_final: 0.6659 (mmt) REVERT: A 167 LEU cc_start: 0.7337 (OUTLIER) cc_final: 0.7088 (tp) REVERT: A 185 MET cc_start: 0.7589 (tpp) cc_final: 0.7209 (tpp) outliers start: 9 outliers final: 7 residues processed: 56 average time/residue: 0.0378 time to fit residues: 2.7754 Evaluate side-chains 55 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 47 time to evaluate : 0.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 189 TRP Chi-restraints excluded: chain A residue 239 PHE Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 476 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 20 optimal weight: 3.9990 chunk 40 optimal weight: 0.5980 chunk 12 optimal weight: 0.9990 chunk 21 optimal weight: 0.6980 chunk 25 optimal weight: 0.9990 chunk 14 optimal weight: 0.9980 chunk 17 optimal weight: 0.1980 chunk 2 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 35 optimal weight: 3.9990 chunk 23 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 430 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4604 r_free = 0.4604 target = 0.209775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.172723 restraints weight = 4579.512| |-----------------------------------------------------------------------------| r_work (start): 0.4401 rms_B_bonded: 3.49 r_work: 0.4274 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.4274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6664 moved from start: 1.4428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 3292 Z= 0.159 Angle : 0.719 11.772 4507 Z= 0.344 Chirality : 0.043 0.154 521 Planarity : 0.006 0.059 547 Dihedral : 4.901 20.406 448 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 2.87 % Allowed : 31.53 % Favored : 65.61 % 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: -0.42 (0.40), residues: 420 helix: 0.43 (0.30), residues: 301 sheet: None (None), residues: 0 loop : -2.03 (0.51), residues: 119 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 39 TYR 0.007 0.001 TYR A 40 PHE 0.014 0.002 PHE A 299 TRP 0.010 0.001 TRP A 292 HIS 0.009 0.002 HIS A 183 Details of bonding type rmsd covalent geometry : bond 0.00355 ( 3292) covalent geometry : angle 0.71946 ( 4507) hydrogen bonds : bond 0.04490 ( 197) hydrogen bonds : angle 4.61351 ( 480) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 55 time to evaluate : 0.109 Fit side-chains REVERT: A 128 TYR cc_start: 0.7798 (t80) cc_final: 0.6649 (m-10) REVERT: A 167 LEU cc_start: 0.7377 (OUTLIER) cc_final: 0.7107 (tp) REVERT: A 185 MET cc_start: 0.7559 (tpp) cc_final: 0.7091 (tpp) REVERT: A 370 ILE cc_start: 0.6834 (tp) cc_final: 0.6482 (tp) outliers start: 9 outliers final: 6 residues processed: 63 average time/residue: 0.0407 time to fit residues: 3.3561 Evaluate side-chains 57 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 50 time to evaluate : 0.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 110 TRP Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 189 TRP Chi-restraints excluded: chain A residue 373 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 18 optimal weight: 0.0030 chunk 20 optimal weight: 7.9990 chunk 16 optimal weight: 0.8980 chunk 34 optimal weight: 0.9980 chunk 29 optimal weight: 0.2980 chunk 0 optimal weight: 9.9990 chunk 22 optimal weight: 0.9990 chunk 5 optimal weight: 0.6980 chunk 37 optimal weight: 0.5980 chunk 6 optimal weight: 0.0270 chunk 41 optimal weight: 0.6980 overall best weight: 0.3248 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4516 r_free = 0.4516 target = 0.196659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.160682 restraints weight = 4679.235| |-----------------------------------------------------------------------------| r_work (start): 0.4332 rms_B_bonded: 3.34 r_work: 0.4211 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.4211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6698 moved from start: 1.4814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3292 Z= 0.131 Angle : 0.666 7.674 4507 Z= 0.323 Chirality : 0.041 0.192 521 Planarity : 0.006 0.059 547 Dihedral : 4.804 18.721 448 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 3.50 % Allowed : 31.53 % Favored : 64.97 % 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: -0.24 (0.41), residues: 420 helix: 0.52 (0.30), residues: 310 sheet: None (None), residues: 0 loop : -1.98 (0.54), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 39 TYR 0.006 0.001 TYR A 40 PHE 0.031 0.001 PHE A 384 TRP 0.010 0.001 TRP A 485 HIS 0.007 0.001 HIS A 414 Details of bonding type rmsd covalent geometry : bond 0.00275 ( 3292) covalent geometry : angle 0.66628 ( 4507) hydrogen bonds : bond 0.04173 ( 197) hydrogen bonds : angle 4.45505 ( 480) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 893.13 seconds wall clock time: 16 minutes 6.82 seconds (966.82 seconds total)