Starting phenix.real_space_refine on Wed Sep 17 03:39:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zne_60269/09_2025/8zne_60269.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zne_60269/09_2025/8zne_60269.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.64 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8zne_60269/09_2025/8zne_60269.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zne_60269/09_2025/8zne_60269.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8zne_60269/09_2025/8zne_60269.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zne_60269/09_2025/8zne_60269.map" } resolution = 2.64 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 3 5.49 5 S 14 5.16 5 C 2098 2.51 5 N 562 2.21 5 O 635 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3312 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3262 Number of conformers: 1 Conformer: "" Number of residues, atoms: 416, 3262 Classifications: {'peptide': 416} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 395} Chain: "A" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 50 Unusual residues: {'NAP': 1} Inner-chain residues flagged as termini: ['pdbres="GLU A 501 "'] Classifications: {'peptide': 1, 'undetermined': 1, 'water': 9} Modifications used: {'COO': 1} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'NAP:plan-2': 1, 'NAP:plan-4': 1} Unresolved non-hydrogen planarities: 12 Time building chain proxies: 0.96, per 1000 atoms: 0.29 Number of scatterers: 3312 At special positions: 0 Unit cell: (66.176, 66.176, 71.44, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 14 16.00 P 3 15.00 O 635 8.00 N 562 7.00 C 2098 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: 0.26 Conformation dependent library (CDL) restraints added in 114.8 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 760 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 2 sheets defined 54.4% alpha, 13.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.16 Creating SS restraints... Processing helix chain 'A' and resid 5 through 18 Processing helix chain 'A' and resid 19 through 21 No H-bonds generated for 'chain 'A' and resid 19 through 21' Processing helix chain 'A' and resid 24 through 32 Processing helix chain 'A' and resid 79 through 97 removed outlier: 3.749A pdb=" N VAL A 97 " --> pdb=" O LYS A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 132 Processing helix chain 'A' and resid 133 through 135 No H-bonds generated for 'chain 'A' and resid 133 through 135' Processing helix chain 'A' and resid 149 through 165 Processing helix chain 'A' and resid 170 through 174 removed outlier: 3.800A pdb=" N ILE A 174 " --> pdb=" O PHE A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 207 Processing helix chain 'A' and resid 221 through 234 Processing helix chain 'A' and resid 256 through 267 removed outlier: 3.512A pdb=" N ARG A 265 " --> pdb=" O LEU A 261 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLU A 266 " --> pdb=" O LYS A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 286 Processing helix chain 'A' and resid 305 through 309 Processing helix chain 'A' and resid 323 through 333 removed outlier: 3.569A pdb=" N ASP A 328 " --> pdb=" O PRO A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 344 Processing helix chain 'A' and resid 345 through 361 Processing helix chain 'A' and resid 365 through 392 Processing helix chain 'A' and resid 394 through 414 Processing sheet with id=AA1, first strand: chain 'A' and resid 36 through 45 removed outlier: 6.666A pdb=" N GLY A 103 " --> pdb=" O HIS A 61 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N LYS A 69 " --> pdb=" O GLY A 104 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N GLY A 106 " --> pdb=" O LYS A 69 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N GLY A 71 " --> pdb=" O GLY A 106 " (cutoff:3.500A) removed outlier: 7.979A pdb=" N ILE A 108 " --> pdb=" O GLY A 71 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N ARG A 73 " --> pdb=" O ILE A 108 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N THR A 68 " --> pdb=" O ILE A 141 " (cutoff:3.500A) removed outlier: 8.120A pdb=" N ALA A 143 " --> pdb=" O THR A 68 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N GLY A 70 " --> pdb=" O ALA A 143 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 277 through 279 removed outlier: 7.902A pdb=" N VAL A 217 " --> pdb=" O VAL A 240 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N VAL A 242 " --> pdb=" O VAL A 217 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N LYS A 214 " --> pdb=" O VAL A 291 " (cutoff:3.500A) removed outlier: 8.247A pdb=" N ALA A 293 " --> pdb=" O LYS A 214 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ALA A 216 " --> pdb=" O ALA A 293 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N LEU A 292 " --> pdb=" O ALA A 315 " (cutoff:3.500A) 179 hydrogen bonds defined for protein. 519 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: 0.51 Time building geometry restraints manager: 0.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 589 1.32 - 1.44: 837 1.44 - 1.57: 1918 1.57 - 1.69: 5 1.69 - 1.81: 27 Bond restraints: 3376 Sorted by residual: bond pdb=" O2B NAP A 500 " pdb=" P2B NAP A 500 " ideal model delta sigma weight residual 1.736 1.610 0.126 2.00e-02 2.50e+03 3.98e+01 bond pdb=" C THR A 280 " pdb=" N ASN A 281 " ideal model delta sigma weight residual 1.334 1.420 -0.086 1.43e-02 4.89e+03 3.58e+01 bond pdb=" N GLY A 254 " pdb=" CA GLY A 254 " ideal model delta sigma weight residual 1.448 1.476 -0.028 8.80e-03 1.29e+04 1.01e+01 bond pdb=" C PRO A 321 " pdb=" O PRO A 321 " ideal model delta sigma weight residual 1.239 1.200 0.038 1.27e-02 6.20e+03 9.10e+00 bond pdb=" C ASP A 327 " pdb=" N ASP A 328 " ideal model delta sigma weight residual 1.335 1.374 -0.039 1.36e-02 5.41e+03 8.11e+00 ... (remaining 3371 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.61: 4346 1.61 - 3.23: 194 3.23 - 4.84: 34 4.84 - 6.46: 5 6.46 - 8.07: 2 Bond angle restraints: 4581 Sorted by residual: angle pdb=" CA GLY A 254 " pdb=" C GLY A 254 " pdb=" O GLY A 254 " ideal model delta sigma weight residual 122.37 118.22 4.15 7.30e-01 1.88e+00 3.24e+01 angle pdb=" CA LYS A 376 " pdb=" C LYS A 376 " pdb=" O LYS A 376 " ideal model delta sigma weight residual 120.42 115.73 4.69 1.06e+00 8.90e-01 1.95e+01 angle pdb=" C SER A 269 " pdb=" CA SER A 269 " pdb=" CB SER A 269 " ideal model delta sigma weight residual 115.89 110.23 5.66 1.32e+00 5.74e-01 1.84e+01 angle pdb=" C PHE A 273 " pdb=" N PRO A 274 " pdb=" CA PRO A 274 " ideal model delta sigma weight residual 119.24 123.04 -3.80 1.04e+00 9.25e-01 1.33e+01 angle pdb=" CA LYS A 376 " pdb=" C LYS A 376 " pdb=" N MET A 377 " ideal model delta sigma weight residual 117.39 121.57 -4.18 1.24e+00 6.50e-01 1.14e+01 ... (remaining 4576 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.79: 1827 16.79 - 33.59: 129 33.59 - 50.38: 51 50.38 - 67.18: 21 67.18 - 83.97: 14 Dihedral angle restraints: 2042 sinusoidal: 851 harmonic: 1191 Sorted by residual: dihedral pdb=" CA TYR A 101 " pdb=" C TYR A 101 " pdb=" N GLY A 102 " pdb=" CA GLY A 102 " ideal model delta harmonic sigma weight residual 180.00 164.04 15.96 0 5.00e+00 4.00e-02 1.02e+01 dihedral pdb=" CA PHE A 341 " pdb=" C PHE A 341 " pdb=" N LEU A 342 " pdb=" CA LEU A 342 " ideal model delta harmonic sigma weight residual 180.00 164.49 15.51 0 5.00e+00 4.00e-02 9.62e+00 dihedral pdb=" CA ASP A 390 " pdb=" CB ASP A 390 " pdb=" CG ASP A 390 " pdb=" OD1 ASP A 390 " ideal model delta sinusoidal sigma weight residual -30.00 -83.03 53.03 1 2.00e+01 2.50e-03 9.57e+00 ... (remaining 2039 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 317 0.034 - 0.068: 117 0.068 - 0.102: 36 0.102 - 0.136: 22 0.136 - 0.170: 6 Chirality restraints: 498 Sorted by residual: chirality pdb=" CA ARG A 187 " pdb=" N ARG A 187 " pdb=" C ARG A 187 " pdb=" CB ARG A 187 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.21e-01 chirality pdb=" CA LEU A 255 " pdb=" N LEU A 255 " pdb=" C LEU A 255 " pdb=" CB LEU A 255 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.46e-01 chirality pdb=" CA VAL A 239 " pdb=" N VAL A 239 " pdb=" C VAL A 239 " pdb=" CB VAL A 239 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.15 2.00e-01 2.50e+01 6.00e-01 ... (remaining 495 not shown) Planarity restraints: 584 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A 149 " 0.032 5.00e-02 4.00e+02 4.77e-02 3.64e+00 pdb=" N PRO A 150 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO A 150 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 150 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 318 " -0.009 2.00e-02 2.50e+03 1.90e-02 3.62e+00 pdb=" C ALA A 318 " 0.033 2.00e-02 2.50e+03 pdb=" O ALA A 318 " -0.013 2.00e-02 2.50e+03 pdb=" N ASN A 319 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 141 " 0.030 5.00e-02 4.00e+02 4.49e-02 3.23e+00 pdb=" N PRO A 142 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO A 142 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 142 " 0.025 5.00e-02 4.00e+02 ... (remaining 581 not shown) Histogram of nonbonded interaction distances: 2.47 - 2.96: 1466 2.96 - 3.44: 3466 3.44 - 3.93: 5883 3.93 - 4.41: 6798 4.41 - 4.90: 10699 Nonbonded interactions: 28312 Sorted by model distance: nonbonded pdb=" OG SER A 351 " pdb=" OE1 GLU A 501 " model vdw 2.472 3.040 nonbonded pdb=" NH2 ARG A 200 " pdb=" OD1 ASP A 374 " model vdw 2.477 3.120 nonbonded pdb=" ND1 HIS A 388 " pdb=" O ILE A 393 " model vdw 2.481 3.120 nonbonded pdb=" OH TYR A 408 " pdb=" O LYS A 419 " model vdw 2.496 3.040 nonbonded pdb=" O LYS A 262 " pdb=" OE1 GLU A 266 " model vdw 2.531 3.040 ... (remaining 28307 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.600 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: 0.020 Extract box with map and model: 0.050 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 4.970 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:9.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 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 0.126 3376 Z= 0.317 Angle : 0.778 8.071 4581 Z= 0.498 Chirality : 0.047 0.170 498 Planarity : 0.005 0.048 584 Dihedral : 16.818 83.970 1282 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.65 % Allowed : 2.35 % Favored : 95.00 % 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: 0.47 (0.41), residues: 414 helix: 1.63 (0.35), residues: 208 sheet: 0.04 (0.68), residues: 65 loop : -1.59 (0.48), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 331 TYR 0.010 0.001 TYR A 363 PHE 0.015 0.002 PHE A 273 TRP 0.008 0.001 TRP A 355 HIS 0.003 0.001 HIS A 388 Details of bonding type rmsd covalent geometry : bond 0.00512 ( 3376) covalent geometry : angle 0.77754 ( 4581) hydrogen bonds : bond 0.14798 ( 179) hydrogen bonds : angle 5.29901 ( 519) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 86 time to evaluate : 0.141 Fit side-chains REVERT: A 9 MET cc_start: 0.7369 (mtp) cc_final: 0.7091 (mtm) outliers start: 9 outliers final: 4 residues processed: 92 average time/residue: 0.7089 time to fit residues: 66.6448 Evaluate side-chains 64 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 60 time to evaluate : 0.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 281 ASN Chi-restraints excluded: chain A residue 329 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 24 optimal weight: 0.7980 chunk 26 optimal weight: 4.9990 chunk 2 optimal weight: 0.0980 chunk 16 optimal weight: 0.9980 chunk 32 optimal weight: 7.9990 chunk 31 optimal weight: 5.9990 chunk 25 optimal weight: 6.9990 chunk 19 optimal weight: 0.9990 chunk 30 optimal weight: 0.7980 chunk 22 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 = 0.3566 r_free = 0.3566 target = 0.139881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.108145 restraints weight = 4165.001| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 1.61 r_work: 0.3000 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2897 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 moved from start: 0.2074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 3376 Z= 0.113 Angle : 0.500 6.444 4581 Z= 0.265 Chirality : 0.043 0.133 498 Planarity : 0.005 0.048 584 Dihedral : 10.632 64.084 496 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.35 % Allowed : 13.82 % Favored : 83.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.84 (0.42), residues: 414 helix: 1.99 (0.36), residues: 209 sheet: 0.07 (0.76), residues: 55 loop : -1.35 (0.48), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 246 TYR 0.007 0.001 TYR A 408 PHE 0.008 0.001 PHE A 381 TRP 0.008 0.001 TRP A 263 HIS 0.003 0.001 HIS A 388 Details of bonding type rmsd covalent geometry : bond 0.00243 ( 3376) covalent geometry : angle 0.49988 ( 4581) hydrogen bonds : bond 0.03987 ( 179) hydrogen bonds : angle 4.12745 ( 519) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 68 time to evaluate : 0.128 Fit side-chains revert: symmetry clash REVERT: A 9 MET cc_start: 0.7811 (mtp) cc_final: 0.7276 (mtm) REVERT: A 327 ASP cc_start: 0.8127 (m-30) cc_final: 0.7913 (m-30) outliers start: 8 outliers final: 0 residues processed: 74 average time/residue: 0.6730 time to fit residues: 51.0918 Evaluate side-chains 62 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 0.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 22 optimal weight: 0.9980 chunk 38 optimal weight: 3.9990 chunk 15 optimal weight: 0.9980 chunk 5 optimal weight: 7.9990 chunk 34 optimal weight: 4.9990 chunk 31 optimal weight: 7.9990 chunk 13 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 24 optimal weight: 5.9990 chunk 17 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 281 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.135471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.103846 restraints weight = 4221.571| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 1.63 r_work: 0.2940 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2836 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8694 moved from start: 0.2711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3376 Z= 0.119 Angle : 0.477 4.841 4581 Z= 0.253 Chirality : 0.043 0.124 498 Planarity : 0.004 0.047 584 Dihedral : 8.792 55.935 490 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.65 % Allowed : 17.94 % Favored : 79.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.96 (0.42), residues: 414 helix: 2.00 (0.36), residues: 213 sheet: 0.09 (0.85), residues: 47 loop : -1.18 (0.48), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 370 TYR 0.007 0.001 TYR A 363 PHE 0.010 0.001 PHE A 341 TRP 0.005 0.001 TRP A 30 HIS 0.004 0.001 HIS A 388 Details of bonding type rmsd covalent geometry : bond 0.00266 ( 3376) covalent geometry : angle 0.47655 ( 4581) hydrogen bonds : bond 0.03988 ( 179) hydrogen bonds : angle 3.90925 ( 519) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 63 time to evaluate : 0.135 Fit side-chains REVERT: A 9 MET cc_start: 0.7923 (mtp) cc_final: 0.7367 (mtm) outliers start: 9 outliers final: 3 residues processed: 69 average time/residue: 0.6576 time to fit residues: 46.5036 Evaluate side-chains 61 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 58 time to evaluate : 0.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ARG Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 233 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 40 optimal weight: 5.9990 chunk 32 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 8 optimal weight: 4.9990 chunk 35 optimal weight: 6.9990 chunk 34 optimal weight: 0.9980 chunk 2 optimal weight: 0.9990 chunk 12 optimal weight: 7.9990 chunk 18 optimal weight: 5.9990 chunk 13 optimal weight: 3.9990 chunk 16 optimal weight: 7.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.132006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.100958 restraints weight = 4231.544| |-----------------------------------------------------------------------------| r_work (start): 0.2986 rms_B_bonded: 1.59 r_work: 0.2881 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.2778 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.2778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8760 moved from start: 0.3205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 3376 Z= 0.163 Angle : 0.534 7.658 4581 Z= 0.283 Chirality : 0.045 0.127 498 Planarity : 0.005 0.047 584 Dihedral : 8.581 57.353 490 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 3.53 % Allowed : 17.35 % Favored : 79.12 % 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: 0.90 (0.42), residues: 414 helix: 1.94 (0.35), residues: 212 sheet: 0.11 (0.84), residues: 47 loop : -1.19 (0.48), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 16 TYR 0.014 0.001 TYR A 363 PHE 0.014 0.002 PHE A 341 TRP 0.008 0.001 TRP A 355 HIS 0.004 0.001 HIS A 388 Details of bonding type rmsd covalent geometry : bond 0.00389 ( 3376) covalent geometry : angle 0.53391 ( 4581) hydrogen bonds : bond 0.04626 ( 179) hydrogen bonds : angle 4.11581 ( 519) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 61 time to evaluate : 0.152 Fit side-chains revert: symmetry clash REVERT: A 9 MET cc_start: 0.7985 (mtp) cc_final: 0.7462 (mtm) REVERT: A 12 LYS cc_start: 0.8296 (tttp) cc_final: 0.7798 (ttpp) REVERT: A 370 ARG cc_start: 0.7150 (ttt-90) cc_final: 0.6229 (ttm170) REVERT: A 388 HIS cc_start: 0.9016 (OUTLIER) cc_final: 0.8446 (t70) outliers start: 12 outliers final: 6 residues processed: 67 average time/residue: 0.6861 time to fit residues: 47.0343 Evaluate side-chains 64 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 57 time to evaluate : 0.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ARG Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 167 LYS Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 264 LYS Chi-restraints excluded: chain A residue 388 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 33 optimal weight: 4.9990 chunk 21 optimal weight: 8.9990 chunk 30 optimal weight: 5.9990 chunk 27 optimal weight: 7.9990 chunk 34 optimal weight: 6.9990 chunk 17 optimal weight: 0.6980 chunk 39 optimal weight: 4.9990 chunk 2 optimal weight: 0.8980 chunk 4 optimal weight: 0.0030 chunk 5 optimal weight: 6.9990 chunk 14 optimal weight: 0.8980 overall best weight: 1.4992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.134510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.103485 restraints weight = 4201.241| |-----------------------------------------------------------------------------| r_work (start): 0.3010 rms_B_bonded: 1.60 r_work: 0.2907 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2805 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8738 moved from start: 0.3314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3376 Z= 0.122 Angle : 0.494 6.060 4581 Z= 0.259 Chirality : 0.043 0.124 498 Planarity : 0.004 0.048 584 Dihedral : 8.292 59.270 490 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 3.24 % Allowed : 18.53 % Favored : 78.24 % 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: 0.99 (0.42), residues: 414 helix: 2.06 (0.35), residues: 213 sheet: 0.11 (0.84), residues: 47 loop : -1.23 (0.48), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 16 TYR 0.011 0.001 TYR A 363 PHE 0.011 0.001 PHE A 341 TRP 0.006 0.001 TRP A 355 HIS 0.003 0.001 HIS A 388 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 3376) covalent geometry : angle 0.49411 ( 4581) hydrogen bonds : bond 0.04048 ( 179) hydrogen bonds : angle 4.00879 ( 519) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 61 time to evaluate : 0.137 Fit side-chains revert: symmetry clash REVERT: A 9 MET cc_start: 0.7996 (mtp) cc_final: 0.7466 (mtm) REVERT: A 244 ASP cc_start: 0.7894 (t0) cc_final: 0.7178 (t0) REVERT: A 304 LYS cc_start: 0.8491 (mmmm) cc_final: 0.8119 (tppp) REVERT: A 370 ARG cc_start: 0.7074 (ttt-90) cc_final: 0.6163 (ttm170) REVERT: A 388 HIS cc_start: 0.8879 (OUTLIER) cc_final: 0.8507 (t70) outliers start: 11 outliers final: 6 residues processed: 66 average time/residue: 0.6262 time to fit residues: 42.3360 Evaluate side-chains 67 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 60 time to evaluate : 0.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ARG Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 264 LYS Chi-restraints excluded: chain A residue 388 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 40 optimal weight: 3.9990 chunk 34 optimal weight: 9.9990 chunk 1 optimal weight: 0.0670 chunk 4 optimal weight: 0.3980 chunk 3 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 19 optimal weight: 0.7980 chunk 25 optimal weight: 7.9990 chunk 6 optimal weight: 3.9990 chunk 27 optimal weight: 5.9990 chunk 14 optimal weight: 0.9980 overall best weight: 0.8520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.135323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.104093 restraints weight = 4251.642| |-----------------------------------------------------------------------------| r_work (start): 0.3039 rms_B_bonded: 1.62 r_work: 0.2935 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2831 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8708 moved from start: 0.3444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 3376 Z= 0.098 Angle : 0.468 7.818 4581 Z= 0.243 Chirality : 0.042 0.125 498 Planarity : 0.004 0.046 584 Dihedral : 7.752 59.689 490 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 3.24 % Allowed : 18.82 % Favored : 77.94 % 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: 1.15 (0.42), residues: 414 helix: 2.25 (0.35), residues: 213 sheet: 0.09 (0.84), residues: 47 loop : -1.21 (0.47), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 16 TYR 0.008 0.001 TYR A 363 PHE 0.009 0.001 PHE A 381 TRP 0.006 0.001 TRP A 63 HIS 0.002 0.000 HIS A 388 Details of bonding type rmsd covalent geometry : bond 0.00212 ( 3376) covalent geometry : angle 0.46798 ( 4581) hydrogen bonds : bond 0.03575 ( 179) hydrogen bonds : angle 3.89834 ( 519) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 62 time to evaluate : 0.131 Fit side-chains REVERT: A 9 MET cc_start: 0.7972 (mtp) cc_final: 0.7451 (mtm) REVERT: A 12 LYS cc_start: 0.8261 (tttp) cc_final: 0.7704 (ttpp) REVERT: A 244 ASP cc_start: 0.7922 (t0) cc_final: 0.7209 (t0) outliers start: 11 outliers final: 5 residues processed: 70 average time/residue: 0.6603 time to fit residues: 47.3121 Evaluate side-chains 65 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 60 time to evaluate : 0.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ARG Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 303 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 13 optimal weight: 0.0570 chunk 9 optimal weight: 5.9990 chunk 15 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 29 optimal weight: 9.9990 chunk 32 optimal weight: 7.9990 chunk 23 optimal weight: 6.9990 chunk 11 optimal weight: 5.9990 chunk 14 optimal weight: 1.9990 chunk 37 optimal weight: 5.9990 overall best weight: 1.6104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.133016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.101602 restraints weight = 4266.078| |-----------------------------------------------------------------------------| r_work (start): 0.3003 rms_B_bonded: 1.64 r_work: 0.2897 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2794 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8736 moved from start: 0.3492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3376 Z= 0.125 Angle : 0.501 7.926 4581 Z= 0.260 Chirality : 0.043 0.122 498 Planarity : 0.004 0.046 584 Dihedral : 7.717 59.889 490 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 4.12 % Allowed : 19.41 % Favored : 76.47 % 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: 1.16 (0.42), residues: 414 helix: 2.27 (0.35), residues: 212 sheet: 0.08 (0.83), residues: 47 loop : -1.21 (0.47), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 16 TYR 0.010 0.001 TYR A 363 PHE 0.011 0.001 PHE A 341 TRP 0.005 0.001 TRP A 355 HIS 0.004 0.001 HIS A 388 Details of bonding type rmsd covalent geometry : bond 0.00287 ( 3376) covalent geometry : angle 0.50067 ( 4581) hydrogen bonds : bond 0.04010 ( 179) hydrogen bonds : angle 3.93569 ( 519) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 57 time to evaluate : 0.144 Fit side-chains REVERT: A 9 MET cc_start: 0.8015 (mtp) cc_final: 0.7519 (mtm) REVERT: A 12 LYS cc_start: 0.8337 (tttp) cc_final: 0.7791 (ttpp) REVERT: A 244 ASP cc_start: 0.7923 (OUTLIER) cc_final: 0.7243 (t0) REVERT: A 370 ARG cc_start: 0.7140 (ttt-90) cc_final: 0.6237 (ttm170) outliers start: 14 outliers final: 8 residues processed: 64 average time/residue: 0.7689 time to fit residues: 50.3074 Evaluate side-chains 64 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 55 time to evaluate : 0.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ARG Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 167 LYS Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 244 ASP Chi-restraints excluded: chain A residue 264 LYS Chi-restraints excluded: chain A residue 303 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 37 optimal weight: 0.7980 chunk 38 optimal weight: 6.9990 chunk 10 optimal weight: 5.9990 chunk 5 optimal weight: 0.9980 chunk 18 optimal weight: 10.0000 chunk 35 optimal weight: 3.9990 chunk 28 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 33 optimal weight: 0.8980 chunk 6 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 HIS A 388 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.136353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.105296 restraints weight = 4242.233| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 1.60 r_work: 0.2954 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2851 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8720 moved from start: 0.3548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 3376 Z= 0.103 Angle : 0.483 7.433 4581 Z= 0.249 Chirality : 0.042 0.125 498 Planarity : 0.004 0.047 584 Dihedral : 7.454 58.489 490 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 3.53 % Allowed : 20.88 % Favored : 75.59 % 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: 1.21 (0.42), residues: 414 helix: 2.32 (0.35), residues: 213 sheet: 0.13 (0.84), residues: 47 loop : -1.22 (0.47), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 16 TYR 0.008 0.001 TYR A 363 PHE 0.009 0.001 PHE A 381 TRP 0.006 0.001 TRP A 63 HIS 0.003 0.001 HIS A 388 Details of bonding type rmsd covalent geometry : bond 0.00230 ( 3376) covalent geometry : angle 0.48287 ( 4581) hydrogen bonds : bond 0.03609 ( 179) hydrogen bonds : angle 3.89305 ( 519) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 58 time to evaluate : 0.138 Fit side-chains REVERT: A 9 MET cc_start: 0.8002 (mtp) cc_final: 0.7497 (mtm) REVERT: A 244 ASP cc_start: 0.7936 (OUTLIER) cc_final: 0.7226 (t0) REVERT: A 332 GLU cc_start: 0.7789 (OUTLIER) cc_final: 0.6992 (mt-10) REVERT: A 370 ARG cc_start: 0.7080 (ttt-90) cc_final: 0.6171 (ttm170) outliers start: 12 outliers final: 6 residues processed: 65 average time/residue: 0.7624 time to fit residues: 50.6718 Evaluate side-chains 64 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 56 time to evaluate : 0.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ARG Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 167 LYS Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 244 ASP Chi-restraints excluded: chain A residue 332 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 23 optimal weight: 7.9990 chunk 3 optimal weight: 6.9990 chunk 38 optimal weight: 4.9990 chunk 4 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 31 optimal weight: 10.0000 chunk 34 optimal weight: 3.9990 chunk 29 optimal weight: 9.9990 chunk 37 optimal weight: 5.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.132844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.102633 restraints weight = 4191.123| |-----------------------------------------------------------------------------| r_work (start): 0.2994 rms_B_bonded: 1.55 r_work: 0.2887 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2785 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8782 moved from start: 0.3585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 3376 Z= 0.176 Angle : 0.548 8.448 4581 Z= 0.287 Chirality : 0.045 0.127 498 Planarity : 0.005 0.047 584 Dihedral : 7.984 59.188 490 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 3.24 % Allowed : 20.88 % Favored : 75.88 % 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: 0.96 (0.42), residues: 414 helix: 2.17 (0.35), residues: 212 sheet: -0.22 (0.79), residues: 52 loop : -1.34 (0.47), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 16 TYR 0.014 0.001 TYR A 363 PHE 0.015 0.002 PHE A 341 TRP 0.007 0.001 TRP A 382 HIS 0.003 0.001 HIS A 388 Details of bonding type rmsd covalent geometry : bond 0.00423 ( 3376) covalent geometry : angle 0.54753 ( 4581) hydrogen bonds : bond 0.04593 ( 179) hydrogen bonds : angle 4.13439 ( 519) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 57 time to evaluate : 0.147 Fit side-chains REVERT: A 9 MET cc_start: 0.8034 (mtp) cc_final: 0.7554 (mtm) REVERT: A 12 LYS cc_start: 0.8422 (tttp) cc_final: 0.7898 (ttpp) REVERT: A 244 ASP cc_start: 0.7942 (OUTLIER) cc_final: 0.7276 (t0) REVERT: A 370 ARG cc_start: 0.7200 (ttt-90) cc_final: 0.6298 (ttm170) outliers start: 11 outliers final: 7 residues processed: 63 average time/residue: 0.7999 time to fit residues: 51.5432 Evaluate side-chains 62 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 54 time to evaluate : 0.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ARG Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 167 LYS Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 244 ASP Chi-restraints excluded: chain A residue 264 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 38 optimal weight: 2.9990 chunk 34 optimal weight: 8.9990 chunk 16 optimal weight: 0.9990 chunk 26 optimal weight: 8.9990 chunk 11 optimal weight: 1.9990 chunk 10 optimal weight: 8.9990 chunk 1 optimal weight: 0.5980 chunk 35 optimal weight: 0.8980 chunk 9 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 HIS 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 = 0.134320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.103365 restraints weight = 4208.399| |-----------------------------------------------------------------------------| r_work (start): 0.3043 rms_B_bonded: 1.58 r_work: 0.2937 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2835 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.2835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8733 moved from start: 0.3641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 3376 Z= 0.109 Angle : 0.500 7.509 4581 Z= 0.259 Chirality : 0.043 0.124 498 Planarity : 0.004 0.047 584 Dihedral : 7.659 59.151 490 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.94 % Allowed : 21.47 % Favored : 75.59 % 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: 1.10 (0.42), residues: 414 helix: 2.24 (0.35), residues: 213 sheet: 0.17 (0.84), residues: 47 loop : -1.34 (0.47), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 396 TYR 0.009 0.001 TYR A 363 PHE 0.009 0.001 PHE A 381 TRP 0.005 0.001 TRP A 30 HIS 0.002 0.000 HIS A 388 Details of bonding type rmsd covalent geometry : bond 0.00247 ( 3376) covalent geometry : angle 0.50043 ( 4581) hydrogen bonds : bond 0.03702 ( 179) hydrogen bonds : angle 3.97194 ( 519) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 56 time to evaluate : 0.129 Fit side-chains REVERT: A 9 MET cc_start: 0.7997 (mtp) cc_final: 0.7493 (mtm) REVERT: A 244 ASP cc_start: 0.7929 (OUTLIER) cc_final: 0.7258 (t0) REVERT: A 272 ASP cc_start: 0.7531 (t0) cc_final: 0.6790 (m-30) REVERT: A 288 GLU cc_start: 0.7837 (tp30) cc_final: 0.7142 (mp0) REVERT: A 370 ARG cc_start: 0.7088 (ttt-90) cc_final: 0.6178 (ttm170) outliers start: 10 outliers final: 7 residues processed: 62 average time/residue: 0.8012 time to fit residues: 50.8568 Evaluate side-chains 63 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 55 time to evaluate : 0.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ARG Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 167 LYS Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 244 ASP Chi-restraints excluded: chain A residue 351 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 2 optimal weight: 0.5980 chunk 10 optimal weight: 3.9990 chunk 36 optimal weight: 4.9990 chunk 31 optimal weight: 8.9990 chunk 7 optimal weight: 7.9990 chunk 23 optimal weight: 8.9990 chunk 5 optimal weight: 2.9990 chunk 15 optimal weight: 5.9990 chunk 8 optimal weight: 0.8980 chunk 38 optimal weight: 4.9990 chunk 26 optimal weight: 9.9990 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.129681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.098209 restraints weight = 4258.365| |-----------------------------------------------------------------------------| r_work (start): 0.2995 rms_B_bonded: 1.62 r_work: 0.2891 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.2789 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8779 moved from start: 0.3667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 3376 Z= 0.174 Angle : 0.553 8.167 4581 Z= 0.290 Chirality : 0.045 0.125 498 Planarity : 0.005 0.048 584 Dihedral : 8.040 59.136 490 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.94 % Allowed : 21.47 % Favored : 75.59 % 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: 0.90 (0.42), residues: 414 helix: 2.13 (0.35), residues: 212 sheet: -0.19 (0.80), residues: 52 loop : -1.43 (0.47), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 396 TYR 0.014 0.001 TYR A 363 PHE 0.015 0.002 PHE A 341 TRP 0.008 0.001 TRP A 382 HIS 0.004 0.001 HIS A 388 Details of bonding type rmsd covalent geometry : bond 0.00419 ( 3376) covalent geometry : angle 0.55336 ( 4581) hydrogen bonds : bond 0.04550 ( 179) hydrogen bonds : angle 4.14887 ( 519) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1602.05 seconds wall clock time: 28 minutes 16.47 seconds (1696.47 seconds total)