Starting phenix.real_space_refine on Tue Mar 3 12:06:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7zz5_15035/03_2026/7zz5_15035.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zz5_15035/03_2026/7zz5_15035.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.43 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7zz5_15035/03_2026/7zz5_15035.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zz5_15035/03_2026/7zz5_15035.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7zz5_15035/03_2026/7zz5_15035.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zz5_15035/03_2026/7zz5_15035.map" } resolution = 2.43 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= 0.008 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 12 5.16 5 C 2291 2.51 5 N 636 2.21 5 O 691 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3633 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 461, 3578 Classifications: {'peptide': 461} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 441} Chain: "A" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 55 Unusual residues: {'ACO': 1, 'BCT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 1.00, per 1000 atoms: 0.28 Number of scatterers: 3633 At special positions: 0 Unit cell: (64.66, 73.14, 74.2, 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 12 16.00 P 3 15.00 O 691 8.00 N 636 7.00 C 2291 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: 0.34 Conformation dependent library (CDL) restraints added in 178.1 milliseconds 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 838 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 5 sheets defined 42.1% alpha, 18.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.12 Creating SS restraints... Processing helix chain 'A' and resid 9 through 23 removed outlier: 3.516A pdb=" N VAL A 14 " --> pdb=" O GLY A 10 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 43 removed outlier: 4.208A pdb=" N PHE A 42 " --> pdb=" O SER A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 60 Processing helix chain 'A' and resid 62 through 74 Processing helix chain 'A' and resid 88 through 98 Processing helix chain 'A' and resid 106 through 114 Processing helix chain 'A' and resid 115 through 126 Processing helix chain 'A' and resid 139 through 150 removed outlier: 3.580A pdb=" N TYR A 150 " --> pdb=" O PHE A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 190 removed outlier: 3.780A pdb=" N HIS A 177 " --> pdb=" O ASP A 173 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLY A 189 " --> pdb=" O SER A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 266 Processing helix chain 'A' and resid 294 through 303 removed outlier: 4.124A pdb=" N THR A 298 " --> pdb=" O GLU A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 315 Processing helix chain 'A' and resid 327 through 331 Processing helix chain 'A' and resid 346 through 350 removed outlier: 3.843A pdb=" N GLY A 350 " --> pdb=" O PRO A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 414 Processing helix chain 'A' and resid 422 through 432 Processing helix chain 'A' and resid 432 through 438 Processing helix chain 'A' and resid 448 through 453 Processing sheet with id=AA1, first strand: chain 'A' and resid 46 through 49 removed outlier: 4.076A pdb=" N VAL A 30 " --> pdb=" O VAL A 6 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 154 through 156 Processing sheet with id=AA3, first strand: chain 'A' and resid 281 through 288 removed outlier: 6.865A pdb=" N GLU A 274 " --> pdb=" O ILE A 285 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N VAL A 287 " --> pdb=" O THR A 272 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N THR A 272 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N HIS A 207 " --> pdb=" O ASP A 227 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N ASP A 227 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N GLU A 209 " --> pdb=" O GLU A 225 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N GLU A 225 " --> pdb=" O GLU A 209 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N GLN A 211 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N SER A 229 " --> pdb=" O ILE A 238 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N ILE A 238 " --> pdb=" O SER A 229 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N GLN A 231 " --> pdb=" O LYS A 236 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N LYS A 236 " --> pdb=" O GLN A 231 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N VAL A 237 " --> pdb=" O ARG A 341 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ARG A 341 " --> pdb=" O VAL A 237 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 356 through 357 removed outlier: 3.526A pdb=" N GLY A 356 " --> pdb=" O VAL A 382 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 360 through 362 172 hydrogen bonds defined for protein. 474 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: 0.76 Time building geometry restraints manager: 0.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 625 1.31 - 1.44: 936 1.44 - 1.57: 2118 1.57 - 1.69: 6 1.69 - 1.82: 18 Bond restraints: 3703 Sorted by residual: bond pdb=" C5A ACO A1201 " pdb=" N7A ACO A1201 " ideal model delta sigma weight residual 1.387 1.520 -0.133 1.00e-02 1.00e+04 1.78e+02 bond pdb=" C6A ACO A1201 " pdb=" N6A ACO A1201 " ideal model delta sigma weight residual 1.337 1.450 -0.113 1.00e-02 1.00e+04 1.29e+02 bond pdb=" C5P ACO A1201 " pdb=" N4P ACO A1201 " ideal model delta sigma weight residual 1.331 1.451 -0.120 1.20e-02 6.94e+03 9.98e+01 bond pdb=" C8A ACO A1201 " pdb=" N9A ACO A1201 " ideal model delta sigma weight residual 1.370 1.270 0.100 1.00e-02 1.00e+04 9.97e+01 bond pdb=" C9P ACO A1201 " pdb=" N8P ACO A1201 " ideal model delta sigma weight residual 1.333 1.453 -0.120 1.30e-02 5.92e+03 8.58e+01 ... (remaining 3698 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.46: 4951 3.46 - 6.93: 41 6.93 - 10.39: 15 10.39 - 13.85: 6 13.85 - 17.32: 3 Bond angle restraints: 5016 Sorted by residual: angle pdb=" C4A ACO A1201 " pdb=" N9A ACO A1201 " pdb=" C8A ACO A1201 " ideal model delta sigma weight residual 105.72 122.31 -16.59 1.00e+00 1.00e+00 2.75e+02 angle pdb=" P1A ACO A1201 " pdb=" O3A ACO A1201 " pdb=" P2A ACO A1201 " ideal model delta sigma weight residual 136.83 124.19 12.64 1.00e+00 1.00e+00 1.60e+02 angle pdb=" CA PRO A 132 " pdb=" N PRO A 132 " pdb=" CD PRO A 132 " ideal model delta sigma weight residual 112.00 95.76 16.24 1.40e+00 5.10e-01 1.35e+02 angle pdb=" N3A ACO A1201 " pdb=" C4A ACO A1201 " pdb=" N9A ACO A1201 " ideal model delta sigma weight residual 127.04 137.47 -10.43 1.15e+00 7.59e-01 8.26e+01 angle pdb=" C ACO A1201 " pdb=" S1P ACO A1201 " pdb=" C2P ACO A1201 " ideal model delta sigma weight residual 101.25 110.12 -8.87 1.00e+00 1.00e+00 7.87e+01 ... (remaining 5011 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.67: 1926 17.67 - 35.33: 222 35.33 - 53.00: 60 53.00 - 70.67: 21 70.67 - 88.34: 11 Dihedral angle restraints: 2240 sinusoidal: 926 harmonic: 1314 Sorted by residual: dihedral pdb=" CA GLU A 175 " pdb=" C GLU A 175 " pdb=" N MET A 176 " pdb=" CA MET A 176 " ideal model delta harmonic sigma weight residual 180.00 158.08 21.92 0 5.00e+00 4.00e-02 1.92e+01 dihedral pdb=" CA ILE A 131 " pdb=" C ILE A 131 " pdb=" N PRO A 132 " pdb=" CA PRO A 132 " ideal model delta harmonic sigma weight residual -180.00 -160.83 -19.17 0 5.00e+00 4.00e-02 1.47e+01 dihedral pdb=" CA TYR A 82 " pdb=" C TYR A 82 " pdb=" N GLY A 83 " pdb=" CA GLY A 83 " ideal model delta harmonic sigma weight residual 180.00 162.13 17.87 0 5.00e+00 4.00e-02 1.28e+01 ... (remaining 2237 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 429 0.057 - 0.113: 106 0.113 - 0.170: 15 0.170 - 0.226: 1 0.226 - 0.283: 3 Chirality restraints: 554 Sorted by residual: chirality pdb=" CA PRO A 132 " pdb=" N PRO A 132 " pdb=" C PRO A 132 " pdb=" CB PRO A 132 " both_signs ideal model delta sigma weight residual False 2.72 2.44 0.28 2.00e-01 2.50e+01 2.00e+00 chirality pdb=" C3B ACO A1201 " pdb=" C2B ACO A1201 " pdb=" C4B ACO A1201 " pdb=" O3B ACO A1201 " both_signs ideal model delta sigma weight residual False -2.76 -2.49 -0.27 2.00e-01 2.50e+01 1.84e+00 chirality pdb=" C2B ACO A1201 " pdb=" C1B ACO A1201 " pdb=" C3B ACO A1201 " pdb=" O2B ACO A1201 " both_signs ideal model delta sigma weight residual False -2.72 -2.47 -0.25 2.00e-01 2.50e+01 1.52e+00 ... (remaining 551 not shown) Planarity restraints: 658 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C BCT A1202 " 0.084 2.00e-02 2.50e+03 4.84e-02 2.34e+01 pdb=" O1 BCT A1202 " -0.031 2.00e-02 2.50e+03 pdb=" O2 BCT A1202 " -0.031 2.00e-02 2.50e+03 pdb=" O3 BCT A1202 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 131 " 0.083 5.00e-02 4.00e+02 1.14e-01 2.07e+01 pdb=" N PRO A 132 " -0.196 5.00e-02 4.00e+02 pdb=" CA PRO A 132 " 0.053 5.00e-02 4.00e+02 pdb=" CD PRO A 132 " 0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 459 " 0.013 2.00e-02 2.50e+03 2.56e-02 6.54e+00 pdb=" C ASP A 459 " -0.044 2.00e-02 2.50e+03 pdb=" O ASP A 459 " 0.017 2.00e-02 2.50e+03 pdb=" N ARG A 460 " 0.015 2.00e-02 2.50e+03 ... (remaining 655 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.78: 816 2.78 - 3.31: 3348 3.31 - 3.84: 6544 3.84 - 4.37: 7545 4.37 - 4.90: 12734 Nonbonded interactions: 30987 Sorted by model distance: nonbonded pdb=" OE2 GLU A 11 " pdb=" OH TYR A 82 " model vdw 2.256 3.040 nonbonded pdb=" OG SER A 329 " pdb=" OE1 GLU A 330 " model vdw 2.332 3.040 nonbonded pdb=" OG1 THR A 296 " pdb=" OE1 GLN A 339 " model vdw 2.333 3.040 nonbonded pdb=" O LYS A 157 " pdb=" NZ LYS A 157 " model vdw 2.346 3.120 nonbonded pdb=" OE1 GLU A 46 " pdb=" OH TYR A 48 " model vdw 2.350 3.040 ... (remaining 30982 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: 1.030 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: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 6.310 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8677 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 : 0.008 0.173 3703 Z= 0.582 Angle : 1.042 17.316 5016 Z= 0.656 Chirality : 0.052 0.283 554 Planarity : 0.006 0.114 658 Dihedral : 17.808 88.336 1402 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 1.86 % Allowed : 16.49 % Favored : 81.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.00 (0.36), residues: 459 helix: -0.40 (0.35), residues: 179 sheet: 0.39 (0.58), residues: 79 loop : -1.26 (0.40), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 458 TYR 0.011 0.001 TYR A 82 PHE 0.028 0.002 PHE A 367 HIS 0.007 0.001 HIS A 222 Details of bonding type rmsd covalent geometry : bond 0.00833 ( 3703) covalent geometry : angle 1.04249 ( 5016) hydrogen bonds : bond 0.17761 ( 172) hydrogen bonds : angle 7.04083 ( 474) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 18 time to evaluate : 0.136 Fit side-chains outliers start: 7 outliers final: 5 residues processed: 24 average time/residue: 0.3590 time to fit residues: 9.1480 Evaluate side-chains 23 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 18 time to evaluate : 0.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ILE Chi-restraints excluded: chain A residue 172 ASN Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 333 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 24 optimal weight: 0.9990 chunk 26 optimal weight: 0.4980 chunk 2 optimal weight: 2.9990 chunk 16 optimal weight: 0.0470 chunk 32 optimal weight: 0.6980 chunk 31 optimal weight: 0.5980 chunk 25 optimal weight: 0.9990 chunk 19 optimal weight: 4.9990 chunk 30 optimal weight: 0.9980 chunk 22 optimal weight: 0.5980 chunk 37 optimal weight: 2.9990 overall best weight: 0.4878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 398 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.065068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.053912 restraints weight = 12723.922| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 2.21 r_work: 0.3060 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2960 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8734 moved from start: 0.0960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 3703 Z= 0.134 Angle : 0.508 8.022 5016 Z= 0.272 Chirality : 0.044 0.136 554 Planarity : 0.003 0.030 658 Dihedral : 10.553 86.423 565 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.13 % Allowed : 15.69 % Favored : 82.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.39), residues: 459 helix: 0.63 (0.38), residues: 187 sheet: 0.89 (0.61), residues: 76 loop : -1.21 (0.42), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 68 TYR 0.007 0.001 TYR A 150 PHE 0.016 0.001 PHE A 191 HIS 0.003 0.001 HIS A 222 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 3703) covalent geometry : angle 0.50819 ( 5016) hydrogen bonds : bond 0.04319 ( 172) hydrogen bonds : angle 5.28722 ( 474) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 18 time to evaluate : 0.149 Fit side-chains REVERT: A 155 MET cc_start: 0.7367 (tmm) cc_final: 0.6835 (tmm) REVERT: A 196 ILE cc_start: 0.4703 (OUTLIER) cc_final: 0.4273 (mp) REVERT: A 405 ARG cc_start: 0.7247 (OUTLIER) cc_final: 0.7010 (tmt170) REVERT: A 414 PHE cc_start: 0.8924 (OUTLIER) cc_final: 0.8224 (t80) outliers start: 8 outliers final: 1 residues processed: 26 average time/residue: 0.4818 time to fit residues: 13.1045 Evaluate side-chains 21 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 17 time to evaluate : 0.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 405 ARG Chi-restraints excluded: chain A residue 414 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 7 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 43 optimal weight: 0.9990 chunk 4 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 33 optimal weight: 0.7980 chunk 44 optimal weight: 0.9990 chunk 27 optimal weight: 0.6980 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 ASN A 224 HIS A 398 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.063756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.052771 restraints weight = 12502.367| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 2.14 r_work: 0.3027 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2929 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8763 moved from start: 0.1165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 3703 Z= 0.190 Angle : 0.519 7.037 5016 Z= 0.281 Chirality : 0.045 0.213 554 Planarity : 0.004 0.033 658 Dihedral : 9.584 87.127 558 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.66 % Allowed : 15.69 % Favored : 81.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.40), residues: 459 helix: 1.01 (0.39), residues: 186 sheet: 0.70 (0.60), residues: 81 loop : -0.98 (0.44), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 460 TYR 0.011 0.001 TYR A 48 PHE 0.014 0.002 PHE A 146 HIS 0.004 0.001 HIS A 222 Details of bonding type rmsd covalent geometry : bond 0.00413 ( 3703) covalent geometry : angle 0.51899 ( 5016) hydrogen bonds : bond 0.04249 ( 172) hydrogen bonds : angle 5.15998 ( 474) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 21 time to evaluate : 0.146 Fit side-chains REVERT: A 155 MET cc_start: 0.7314 (OUTLIER) cc_final: 0.6726 (tmm) REVERT: A 196 ILE cc_start: 0.5067 (OUTLIER) cc_final: 0.4658 (mp) REVERT: A 414 PHE cc_start: 0.8912 (OUTLIER) cc_final: 0.8333 (t80) outliers start: 10 outliers final: 2 residues processed: 30 average time/residue: 0.3952 time to fit residues: 12.4879 Evaluate side-chains 22 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 17 time to evaluate : 0.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 414 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 16 optimal weight: 6.9990 chunk 0 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 29 optimal weight: 0.1980 chunk 23 optimal weight: 0.5980 chunk 5 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 24 optimal weight: 0.6980 chunk 26 optimal weight: 0.5980 chunk 37 optimal weight: 3.9990 chunk 27 optimal weight: 0.5980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 ASN A 398 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.064473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.053498 restraints weight = 12578.272| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 2.17 r_work: 0.3048 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2949 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8745 moved from start: 0.1208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3703 Z= 0.133 Angle : 0.496 8.095 5016 Z= 0.263 Chirality : 0.044 0.157 554 Planarity : 0.003 0.028 658 Dihedral : 9.273 84.398 558 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 3.46 % Allowed : 14.89 % Favored : 81.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.36 (0.40), residues: 459 helix: 1.16 (0.39), residues: 187 sheet: 0.82 (0.60), residues: 81 loop : -0.93 (0.45), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 171 TYR 0.016 0.001 TYR A 150 PHE 0.012 0.001 PHE A 191 HIS 0.003 0.001 HIS A 222 Details of bonding type rmsd covalent geometry : bond 0.00288 ( 3703) covalent geometry : angle 0.49558 ( 5016) hydrogen bonds : bond 0.03694 ( 172) hydrogen bonds : angle 4.98369 ( 474) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 20 time to evaluate : 0.139 Fit side-chains REVERT: A 57 ILE cc_start: 0.9314 (OUTLIER) cc_final: 0.8934 (tp) REVERT: A 155 MET cc_start: 0.7293 (OUTLIER) cc_final: 0.6706 (tmm) REVERT: A 414 PHE cc_start: 0.8924 (OUTLIER) cc_final: 0.8375 (t80) REVERT: A 458 ARG cc_start: 0.8371 (OUTLIER) cc_final: 0.8050 (mtm-85) outliers start: 13 outliers final: 4 residues processed: 31 average time/residue: 0.5509 time to fit residues: 17.6886 Evaluate side-chains 26 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 18 time to evaluate : 0.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ILE Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 263 LYS Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 414 PHE Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 458 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 34 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 chunk 33 optimal weight: 0.7980 chunk 18 optimal weight: 4.9990 chunk 16 optimal weight: 6.9990 chunk 31 optimal weight: 0.9990 chunk 38 optimal weight: 0.6980 chunk 6 optimal weight: 0.3980 chunk 44 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 ASN A 177 HIS A 398 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.063987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.052988 restraints weight = 12561.261| |-----------------------------------------------------------------------------| r_work (start): 0.3129 rms_B_bonded: 2.17 r_work: 0.3031 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2934 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8759 moved from start: 0.1370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 3703 Z= 0.169 Angle : 0.516 7.298 5016 Z= 0.276 Chirality : 0.045 0.141 554 Planarity : 0.003 0.030 658 Dihedral : 9.213 84.310 558 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 2.39 % Allowed : 16.76 % Favored : 80.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.40), residues: 459 helix: 1.21 (0.39), residues: 186 sheet: 0.84 (0.60), residues: 81 loop : -0.93 (0.45), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 68 TYR 0.009 0.001 TYR A 150 PHE 0.008 0.002 PHE A 42 HIS 0.007 0.001 HIS A 177 Details of bonding type rmsd covalent geometry : bond 0.00370 ( 3703) covalent geometry : angle 0.51579 ( 5016) hydrogen bonds : bond 0.03898 ( 172) hydrogen bonds : angle 5.04085 ( 474) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 24 time to evaluate : 0.146 Fit side-chains REVERT: A 57 ILE cc_start: 0.9309 (OUTLIER) cc_final: 0.8933 (tp) REVERT: A 155 MET cc_start: 0.7282 (OUTLIER) cc_final: 0.6691 (tmm) REVERT: A 414 PHE cc_start: 0.8927 (OUTLIER) cc_final: 0.8370 (t80) outliers start: 9 outliers final: 4 residues processed: 32 average time/residue: 0.4181 time to fit residues: 14.0214 Evaluate side-chains 27 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 20 time to evaluate : 0.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ILE Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 414 PHE Chi-restraints excluded: chain A residue 457 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 14 optimal weight: 0.3980 chunk 13 optimal weight: 5.9990 chunk 39 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 9 optimal weight: 0.0980 chunk 11 optimal weight: 1.9990 chunk 6 optimal weight: 0.6980 chunk 31 optimal weight: 0.9980 chunk 33 optimal weight: 0.7980 chunk 21 optimal weight: 0.9990 chunk 26 optimal weight: 0.7980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 ASN A 398 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.064488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.053482 restraints weight = 12551.424| |-----------------------------------------------------------------------------| r_work (start): 0.3143 rms_B_bonded: 2.18 r_work: 0.3043 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2944 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8749 moved from start: 0.1422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3703 Z= 0.136 Angle : 0.516 8.860 5016 Z= 0.270 Chirality : 0.045 0.156 554 Planarity : 0.003 0.024 658 Dihedral : 9.062 83.673 558 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.39 % Allowed : 16.76 % Favored : 80.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.40), residues: 459 helix: 1.30 (0.39), residues: 186 sheet: 0.90 (0.60), residues: 81 loop : -0.98 (0.45), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 171 TYR 0.008 0.001 TYR A 150 PHE 0.015 0.001 PHE A 191 HIS 0.003 0.001 HIS A 222 Details of bonding type rmsd covalent geometry : bond 0.00295 ( 3703) covalent geometry : angle 0.51577 ( 5016) hydrogen bonds : bond 0.03635 ( 172) hydrogen bonds : angle 4.96860 ( 474) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 22 time to evaluate : 0.149 Fit side-chains REVERT: A 57 ILE cc_start: 0.9306 (OUTLIER) cc_final: 0.8946 (tp) REVERT: A 155 MET cc_start: 0.7250 (OUTLIER) cc_final: 0.6636 (tmm) REVERT: A 414 PHE cc_start: 0.8843 (OUTLIER) cc_final: 0.8310 (t80) REVERT: A 458 ARG cc_start: 0.8355 (OUTLIER) cc_final: 0.8005 (mtm-85) outliers start: 9 outliers final: 4 residues processed: 30 average time/residue: 0.4359 time to fit residues: 13.6739 Evaluate side-chains 27 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 19 time to evaluate : 0.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ILE Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 414 PHE Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 458 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 30 optimal weight: 1.9990 chunk 29 optimal weight: 0.5980 chunk 36 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 38 optimal weight: 0.0870 chunk 4 optimal weight: 0.8980 chunk 7 optimal weight: 2.9990 chunk 42 optimal weight: 0.8980 chunk 16 optimal weight: 0.0070 chunk 15 optimal weight: 0.7980 chunk 39 optimal weight: 1.9990 overall best weight: 0.4776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 398 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.064769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.053723 restraints weight = 12677.173| |-----------------------------------------------------------------------------| r_work (start): 0.3151 rms_B_bonded: 2.20 r_work: 0.3050 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2951 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8746 moved from start: 0.1462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3703 Z= 0.127 Angle : 0.519 9.202 5016 Z= 0.272 Chirality : 0.044 0.154 554 Planarity : 0.003 0.023 658 Dihedral : 8.884 84.085 558 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 2.13 % Allowed : 17.55 % Favored : 80.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.40), residues: 459 helix: 1.29 (0.39), residues: 187 sheet: 0.93 (0.60), residues: 81 loop : -0.94 (0.45), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 171 TYR 0.008 0.001 TYR A 150 PHE 0.007 0.001 PHE A 191 HIS 0.003 0.001 HIS A 222 Details of bonding type rmsd covalent geometry : bond 0.00273 ( 3703) covalent geometry : angle 0.51878 ( 5016) hydrogen bonds : bond 0.03539 ( 172) hydrogen bonds : angle 4.95280 ( 474) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 22 time to evaluate : 0.145 Fit side-chains REVERT: A 57 ILE cc_start: 0.9294 (OUTLIER) cc_final: 0.8955 (tp) REVERT: A 155 MET cc_start: 0.7280 (OUTLIER) cc_final: 0.6753 (tmm) REVERT: A 414 PHE cc_start: 0.8847 (OUTLIER) cc_final: 0.8307 (t80) outliers start: 8 outliers final: 4 residues processed: 28 average time/residue: 0.4517 time to fit residues: 13.2690 Evaluate side-chains 27 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 20 time to evaluate : 0.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ILE Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 263 LYS Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 414 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 19 optimal weight: 3.9990 chunk 8 optimal weight: 0.0020 chunk 37 optimal weight: 4.9990 chunk 4 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 41 optimal weight: 0.7980 chunk 35 optimal weight: 0.6980 chunk 27 optimal weight: 0.7980 chunk 33 optimal weight: 0.5980 chunk 24 optimal weight: 0.6980 chunk 10 optimal weight: 0.1980 overall best weight: 0.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 ASN A 398 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.064943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.053902 restraints weight = 12605.704| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 2.19 r_work: 0.3057 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2957 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8740 moved from start: 0.1492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3703 Z= 0.119 Angle : 0.516 9.076 5016 Z= 0.270 Chirality : 0.044 0.155 554 Planarity : 0.003 0.022 658 Dihedral : 8.807 83.038 558 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.86 % Allowed : 18.62 % Favored : 79.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.40), residues: 459 helix: 1.33 (0.39), residues: 187 sheet: 0.85 (0.60), residues: 82 loop : -0.96 (0.45), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 460 TYR 0.007 0.001 TYR A 150 PHE 0.015 0.001 PHE A 191 HIS 0.003 0.001 HIS A 222 Details of bonding type rmsd covalent geometry : bond 0.00257 ( 3703) covalent geometry : angle 0.51552 ( 5016) hydrogen bonds : bond 0.03450 ( 172) hydrogen bonds : angle 4.92300 ( 474) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 19 time to evaluate : 0.097 Fit side-chains REVERT: A 57 ILE cc_start: 0.9275 (OUTLIER) cc_final: 0.8953 (tp) REVERT: A 155 MET cc_start: 0.7277 (OUTLIER) cc_final: 0.6758 (tmm) REVERT: A 176 MET cc_start: 0.6408 (mmt) cc_final: 0.6135 (mpm) REVERT: A 414 PHE cc_start: 0.8821 (OUTLIER) cc_final: 0.8266 (t80) outliers start: 7 outliers final: 4 residues processed: 25 average time/residue: 0.4260 time to fit residues: 11.1456 Evaluate side-chains 25 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 18 time to evaluate : 0.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ILE Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 263 LYS Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 414 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 34 optimal weight: 0.8980 chunk 33 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 chunk 39 optimal weight: 2.9990 chunk 3 optimal weight: 0.6980 chunk 42 optimal weight: 0.5980 chunk 10 optimal weight: 0.5980 chunk 43 optimal weight: 0.0470 chunk 45 optimal weight: 0.6980 chunk 44 optimal weight: 1.9990 chunk 38 optimal weight: 0.6980 overall best weight: 0.5278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 398 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.064436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.053750 restraints weight = 12528.671| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 2.10 r_work: 0.3060 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2964 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8728 moved from start: 0.1504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3703 Z= 0.132 Angle : 0.525 8.956 5016 Z= 0.274 Chirality : 0.044 0.155 554 Planarity : 0.004 0.059 658 Dihedral : 9.042 77.811 558 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.39 % Allowed : 17.82 % Favored : 79.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.40), residues: 459 helix: 1.32 (0.39), residues: 187 sheet: 0.86 (0.60), residues: 82 loop : -0.92 (0.45), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 460 TYR 0.007 0.001 TYR A 150 PHE 0.007 0.001 PHE A 275 HIS 0.003 0.001 HIS A 222 Details of bonding type rmsd covalent geometry : bond 0.00285 ( 3703) covalent geometry : angle 0.52468 ( 5016) hydrogen bonds : bond 0.03528 ( 172) hydrogen bonds : angle 4.93107 ( 474) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 18 time to evaluate : 0.094 Fit side-chains REVERT: A 57 ILE cc_start: 0.9250 (OUTLIER) cc_final: 0.8923 (tp) REVERT: A 155 MET cc_start: 0.7262 (OUTLIER) cc_final: 0.6748 (tmm) REVERT: A 414 PHE cc_start: 0.8771 (OUTLIER) cc_final: 0.8224 (t80) outliers start: 9 outliers final: 4 residues processed: 26 average time/residue: 0.4420 time to fit residues: 12.0518 Evaluate side-chains 25 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 18 time to evaluate : 0.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ILE Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 263 LYS Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 414 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 2 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 chunk 41 optimal weight: 0.5980 chunk 45 optimal weight: 0.0370 chunk 26 optimal weight: 0.6980 chunk 17 optimal weight: 0.5980 chunk 18 optimal weight: 0.4980 chunk 9 optimal weight: 0.5980 chunk 24 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 35 optimal weight: 0.6980 overall best weight: 0.4658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 ASN A 398 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.064640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.053841 restraints weight = 12783.767| |-----------------------------------------------------------------------------| r_work (start): 0.3160 rms_B_bonded: 2.13 r_work: 0.3065 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2969 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8724 moved from start: 0.1584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3703 Z= 0.124 Angle : 0.536 9.006 5016 Z= 0.281 Chirality : 0.045 0.160 554 Planarity : 0.003 0.039 658 Dihedral : 8.827 79.071 558 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.86 % Allowed : 18.62 % Favored : 79.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.40), residues: 459 helix: 1.34 (0.39), residues: 187 sheet: 1.24 (0.63), residues: 72 loop : -0.86 (0.44), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 458 TYR 0.006 0.001 TYR A 82 PHE 0.020 0.001 PHE A 191 HIS 0.003 0.001 HIS A 222 Details of bonding type rmsd covalent geometry : bond 0.00267 ( 3703) covalent geometry : angle 0.53608 ( 5016) hydrogen bonds : bond 0.03486 ( 172) hydrogen bonds : angle 4.99165 ( 474) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 23 time to evaluate : 0.122 Fit side-chains revert: symmetry clash REVERT: A 57 ILE cc_start: 0.9241 (OUTLIER) cc_final: 0.8913 (tp) REVERT: A 155 MET cc_start: 0.7256 (OUTLIER) cc_final: 0.6738 (tmm) REVERT: A 176 MET cc_start: 0.6615 (mmt) cc_final: 0.6406 (mpm) REVERT: A 414 PHE cc_start: 0.8764 (OUTLIER) cc_final: 0.8218 (t80) outliers start: 7 outliers final: 4 residues processed: 29 average time/residue: 0.4659 time to fit residues: 14.1559 Evaluate side-chains 27 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 20 time to evaluate : 0.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ILE Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 263 LYS Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 414 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 30 optimal weight: 2.9990 chunk 32 optimal weight: 0.8980 chunk 13 optimal weight: 0.4980 chunk 20 optimal weight: 1.9990 chunk 12 optimal weight: 4.9990 chunk 24 optimal weight: 0.6980 chunk 35 optimal weight: 2.9990 chunk 40 optimal weight: 0.5980 chunk 9 optimal weight: 0.6980 chunk 29 optimal weight: 0.3980 chunk 3 optimal weight: 1.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 398 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.064351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.053621 restraints weight = 12549.443| |-----------------------------------------------------------------------------| r_work (start): 0.3152 rms_B_bonded: 2.10 r_work: 0.3058 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2962 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8731 moved from start: 0.1554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3703 Z= 0.141 Angle : 0.560 9.444 5016 Z= 0.293 Chirality : 0.045 0.155 554 Planarity : 0.003 0.041 658 Dihedral : 9.013 77.540 558 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 1.86 % Allowed : 19.15 % Favored : 78.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.40), residues: 459 helix: 1.30 (0.39), residues: 187 sheet: 1.21 (0.63), residues: 72 loop : -0.88 (0.44), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 168 TYR 0.007 0.001 TYR A 48 PHE 0.007 0.001 PHE A 42 HIS 0.003 0.001 HIS A 222 Details of bonding type rmsd covalent geometry : bond 0.00307 ( 3703) covalent geometry : angle 0.56039 ( 5016) hydrogen bonds : bond 0.03608 ( 172) hydrogen bonds : angle 5.03763 ( 474) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1529.79 seconds wall clock time: 26 minutes 45.26 seconds (1605.26 seconds total)