Starting phenix.real_space_refine on Fri Oct 10 10:41:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qrp_18622/10_2025/8qrp_18622.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qrp_18622/10_2025/8qrp_18622.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8qrp_18622/10_2025/8qrp_18622.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qrp_18622/10_2025/8qrp_18622.map" model { file = "/net/cci-nas-00/data/ceres_data/8qrp_18622/10_2025/8qrp_18622.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qrp_18622/10_2025/8qrp_18622.cif" } resolution = 2.7 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= 1.000 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 S 15 5.16 5 Na 3 4.78 5 C 2049 2.51 5 N 511 2.21 5 O 545 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-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3123 Number of models: 1 Model: "" Number of chains: 2 Chain: "B" Number of atoms: 3110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3110 Classifications: {'peptide': 419} Link IDs: {'PTRANS': 16, 'TRANS': 402} Chain breaks: 2 Chain: "B" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 13 Unusual residues: {' NA': 3} Classifications: {'peptide': 1, 'undetermined': 3} Modifications used: {'COO': 1} Link IDs: {None: 3} Time building chain proxies: 0.99, per 1000 atoms: 0.32 Number of scatterers: 3123 At special positions: 0 Unit cell: (62.7, 71.896, 74.404, 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 15 16.00 Na 3 11.00 O 545 8.00 N 511 7.00 C 2049 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: 0.19 Conformation dependent library (CDL) restraints added in 133.5 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 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: 20 helices and 1 sheets defined 86.7% alpha, 3.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.10 Creating SS restraints... Processing helix chain 'B' and resid 49 through 76 Processing helix chain 'B' and resid 76 through 82 removed outlier: 3.565A pdb=" N ALA B 80 " --> pdb=" O GLY B 76 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU B 81 " --> pdb=" O GLY B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 103 removed outlier: 4.283A pdb=" N ALA B 88 " --> pdb=" O GLU B 84 " (cutoff:3.500A) Proline residue: B 92 - end of helix removed outlier: 3.684A pdb=" N ILE B 103 " --> pdb=" O LEU B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 118 Processing helix chain 'B' and resid 120 through 154 Processing helix chain 'B' and resid 179 through 192 Processing helix chain 'B' and resid 195 through 200 Processing helix chain 'B' and resid 230 through 249 removed outlier: 3.723A pdb=" N GLY B 249 " --> pdb=" O LEU B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 292 removed outlier: 3.802A pdb=" N TRP B 275 " --> pdb=" O SER B 271 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N TYR B 276 " --> pdb=" O TRP B 272 " (cutoff:3.500A) Proline residue: B 278 - end of helix removed outlier: 3.506A pdb=" N LYS B 288 " --> pdb=" O LEU B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 302 removed outlier: 3.556A pdb=" N ARG B 301 " --> pdb=" O LEU B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 319 Processing helix chain 'B' and resid 319 through 329 Processing helix chain 'B' and resid 332 through 340 removed outlier: 3.592A pdb=" N PHE B 336 " --> pdb=" O ASN B 332 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ILE B 340 " --> pdb=" O PHE B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 340 through 351 Processing helix chain 'B' and resid 352 through 367 removed outlier: 3.596A pdb=" N THR B 356 " --> pdb=" O SER B 352 " (cutoff:3.500A) Proline residue: B 358 - end of helix Processing helix chain 'B' and resid 371 through 386 Proline residue: B 380 - end of helix removed outlier: 3.987A pdb=" N THR B 384 " --> pdb=" O PRO B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 387 through 405 Processing helix chain 'B' and resid 410 through 428 Processing helix chain 'B' and resid 438 through 447 removed outlier: 3.671A pdb=" N ILE B 442 " --> pdb=" O THR B 438 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 487 removed outlier: 3.867A pdb=" N ILE B 456 " --> pdb=" O HIS B 452 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA B 458 " --> pdb=" O SER B 454 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N VAL B 459 " --> pdb=" O LEU B 455 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N TRP B 461 " --> pdb=" O LEU B 457 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N LEU B 462 " --> pdb=" O ALA B 458 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ARG B 465 " --> pdb=" O TRP B 461 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ASP B 475 " --> pdb=" O ASN B 471 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ASN B 484 " --> pdb=" O GLY B 480 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N TYR B 485 " --> pdb=" O LEU B 481 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 202 through 210 257 hydrogen bonds defined for protein. 771 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: 0.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 989 1.34 - 1.46: 519 1.46 - 1.57: 1643 1.57 - 1.69: 0 1.69 - 1.81: 24 Bond restraints: 3175 Sorted by residual: bond pdb=" CB MET B 274 " pdb=" CG MET B 274 " ideal model delta sigma weight residual 1.520 1.499 0.021 3.00e-02 1.11e+03 5.02e-01 bond pdb=" CA ARG B 330 " pdb=" C ARG B 330 " ideal model delta sigma weight residual 1.531 1.523 0.008 1.12e-02 7.97e+03 4.92e-01 bond pdb=" C PHE B 91 " pdb=" N PRO B 92 " ideal model delta sigma weight residual 1.335 1.342 -0.007 1.28e-02 6.10e+03 3.40e-01 bond pdb=" C VAL B 472 " pdb=" O VAL B 472 " ideal model delta sigma weight residual 1.240 1.233 0.007 1.18e-02 7.18e+03 3.08e-01 bond pdb=" CA VAL B 459 " pdb=" CB VAL B 459 " ideal model delta sigma weight residual 1.537 1.544 -0.007 1.30e-02 5.92e+03 2.84e-01 ... (remaining 3170 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.24: 4225 1.24 - 2.49: 76 2.49 - 3.73: 15 3.73 - 4.98: 6 4.98 - 6.22: 2 Bond angle restraints: 4324 Sorted by residual: angle pdb=" C VAL B 295 " pdb=" N GLY B 296 " pdb=" CA GLY B 296 " ideal model delta sigma weight residual 119.98 121.98 -2.00 1.11e+00 8.12e-01 3.26e+00 angle pdb=" CA LEU B 297 " pdb=" CB LEU B 297 " pdb=" CG LEU B 297 " ideal model delta sigma weight residual 116.30 122.52 -6.22 3.50e+00 8.16e-02 3.16e+00 angle pdb=" N PHE B 299 " pdb=" CA PHE B 299 " pdb=" C PHE B 299 " ideal model delta sigma weight residual 113.20 111.08 2.12 1.21e+00 6.83e-01 3.08e+00 angle pdb=" C VAL B 459 " pdb=" CA VAL B 459 " pdb=" CB VAL B 459 " ideal model delta sigma weight residual 111.85 109.86 1.99 1.27e+00 6.20e-01 2.45e+00 angle pdb=" C LEU B 70 " pdb=" N GLY B 71 " pdb=" CA GLY B 71 " ideal model delta sigma weight residual 119.94 121.57 -1.63 1.11e+00 8.12e-01 2.16e+00 ... (remaining 4319 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.76: 1593 13.76 - 27.51: 202 27.51 - 41.26: 50 41.26 - 55.02: 15 55.02 - 68.77: 3 Dihedral angle restraints: 1863 sinusoidal: 680 harmonic: 1183 Sorted by residual: dihedral pdb=" CA GLU B 225 " pdb=" CB GLU B 225 " pdb=" CG GLU B 225 " pdb=" CD GLU B 225 " ideal model delta sinusoidal sigma weight residual -180.00 -121.99 -58.01 3 1.50e+01 4.44e-03 9.46e+00 dihedral pdb=" N LYS B 219 " pdb=" CA LYS B 219 " pdb=" CB LYS B 219 " pdb=" CG LYS B 219 " ideal model delta sinusoidal sigma weight residual -60.00 -112.41 52.41 3 1.50e+01 4.44e-03 9.11e+00 dihedral pdb=" CA ILE B 231 " pdb=" CB ILE B 231 " pdb=" CG1 ILE B 231 " pdb=" CD1 ILE B 231 " ideal model delta sinusoidal sigma weight residual 180.00 127.88 52.12 3 1.50e+01 4.44e-03 9.08e+00 ... (remaining 1860 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 365 0.027 - 0.053: 98 0.053 - 0.080: 57 0.080 - 0.107: 18 0.107 - 0.133: 4 Chirality restraints: 542 Sorted by residual: chirality pdb=" CA ILE B 431 " pdb=" N ILE B 431 " pdb=" C ILE B 431 " pdb=" CB ILE B 431 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.44e-01 chirality pdb=" CA VAL B 220 " pdb=" N VAL B 220 " pdb=" C VAL B 220 " pdb=" CB VAL B 220 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.71e-01 chirality pdb=" CA THR B 342 " pdb=" N THR B 342 " pdb=" C THR B 342 " pdb=" CB THR B 342 " both_signs ideal model delta sigma weight residual False 2.53 2.42 0.11 2.00e-01 2.50e+01 3.03e-01 ... (remaining 539 not shown) Planarity restraints: 535 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 357 " -0.029 5.00e-02 4.00e+02 4.39e-02 3.08e+00 pdb=" N PRO B 358 " 0.076 5.00e-02 4.00e+02 pdb=" CA PRO B 358 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 358 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP B 120 " -0.023 5.00e-02 4.00e+02 3.51e-02 1.97e+00 pdb=" N PRO B 121 " 0.061 5.00e-02 4.00e+02 pdb=" CA PRO B 121 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 121 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 91 " -0.016 5.00e-02 4.00e+02 2.35e-02 8.85e-01 pdb=" N PRO B 92 " 0.041 5.00e-02 4.00e+02 pdb=" CA PRO B 92 " -0.012 5.00e-02 4.00e+02 pdb=" CD PRO B 92 " -0.013 5.00e-02 4.00e+02 ... (remaining 532 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 856 2.81 - 3.33: 3193 3.33 - 3.85: 5339 3.85 - 4.38: 6178 4.38 - 4.90: 10860 Nonbonded interactions: 26426 Sorted by model distance: nonbonded pdb=" OG1 THR B 139 " pdb="NA NA B 603 " model vdw 2.285 2.470 nonbonded pdb=" OD1 ASN B 386 " pdb="NA NA B 603 " model vdw 2.292 2.470 nonbonded pdb=" OD1 ASP B 388 " pdb="NA NA B 603 " model vdw 2.303 2.470 nonbonded pdb=" OG SER B 353 " pdb=" OXT GLN B 604 " model vdw 2.304 3.040 nonbonded pdb=" O PHE B 135 " pdb="NA NA B 603 " model vdw 2.315 2.470 ... (remaining 26421 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: 0.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.060 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 4.860 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 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 : 0.002 0.025 3175 Z= 0.106 Angle : 0.474 6.222 4324 Z= 0.262 Chirality : 0.035 0.133 542 Planarity : 0.004 0.044 535 Dihedral : 13.506 68.775 1103 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 0.00 % Allowed : 16.41 % Favored : 83.59 % 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: 1.62 (0.41), residues: 413 helix: 1.58 (0.28), residues: 325 sheet: 0.09 (1.38), residues: 20 loop : -0.97 (0.65), residues: 68 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 301 TYR 0.007 0.001 TYR B 208 PHE 0.012 0.001 PHE B 393 TRP 0.007 0.001 TRP B 130 HIS 0.001 0.000 HIS B 373 Details of bonding type rmsd covalent geometry : bond 0.00236 ( 3175) covalent geometry : angle 0.47361 ( 4324) hydrogen bonds : bond 0.20658 ( 257) hydrogen bonds : angle 7.07678 ( 771) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.128 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 43 average time/residue: 0.5798 time to fit residues: 25.7230 Evaluate side-chains 41 residues out of total 329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 24 optimal weight: 0.8980 chunk 26 optimal weight: 0.9980 chunk 2 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 31 optimal weight: 0.6980 chunk 25 optimal weight: 0.7980 chunk 19 optimal weight: 0.0980 chunk 30 optimal weight: 0.6980 chunk 22 optimal weight: 0.9990 chunk 37 optimal weight: 0.0870 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 224 GLN B 263 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.145502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.112159 restraints weight = 3751.983| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 1.81 r_work: 0.3285 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3177 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.1523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3175 Z= 0.130 Angle : 0.492 5.068 4324 Z= 0.252 Chirality : 0.037 0.133 542 Planarity : 0.005 0.042 535 Dihedral : 3.354 16.206 440 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 3.65 % Allowed : 13.98 % Favored : 82.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.32 (0.42), residues: 413 helix: 2.03 (0.29), residues: 333 sheet: -0.31 (1.27), residues: 20 loop : -0.56 (0.81), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 301 TYR 0.009 0.002 TYR B 276 PHE 0.010 0.001 PHE B 237 TRP 0.008 0.001 TRP B 338 HIS 0.001 0.001 HIS B 313 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 3175) covalent geometry : angle 0.49233 ( 4324) hydrogen bonds : bond 0.04553 ( 257) hydrogen bonds : angle 4.80319 ( 771) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 51 time to evaluate : 0.120 Fit side-chains REVERT: B 251 GLU cc_start: 0.8167 (OUTLIER) cc_final: 0.7446 (tt0) REVERT: B 253 GLU cc_start: 0.8072 (mt-10) cc_final: 0.7590 (mm-30) REVERT: B 475 ASP cc_start: 0.7721 (m-30) cc_final: 0.7519 (m-30) outliers start: 12 outliers final: 5 residues processed: 56 average time/residue: 0.4896 time to fit residues: 28.2652 Evaluate side-chains 51 residues out of total 329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 45 time to evaluate : 0.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 251 GLU Chi-restraints excluded: chain B residue 384 THR Chi-restraints excluded: chain B residue 436 VAL Chi-restraints excluded: chain B residue 438 THR Chi-restraints excluded: chain B residue 457 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 3 optimal weight: 4.9990 chunk 33 optimal weight: 0.5980 chunk 4 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 40 optimal weight: 0.6980 chunk 18 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 chunk 32 optimal weight: 0.6980 chunk 8 optimal weight: 0.7980 chunk 7 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 224 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.145092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.108577 restraints weight = 3700.852| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 1.90 r_work: 0.3270 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3165 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.1719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3175 Z= 0.141 Angle : 0.476 5.019 4324 Z= 0.245 Chirality : 0.038 0.137 542 Planarity : 0.004 0.040 535 Dihedral : 3.256 14.086 440 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 3.95 % Allowed : 14.29 % Favored : 81.76 % 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: 2.42 (0.42), residues: 413 helix: 2.15 (0.28), residues: 332 sheet: -0.45 (1.20), residues: 20 loop : -0.74 (0.82), residues: 61 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 301 TYR 0.009 0.002 TYR B 208 PHE 0.011 0.001 PHE B 237 TRP 0.011 0.001 TRP B 338 HIS 0.001 0.000 HIS B 313 Details of bonding type rmsd covalent geometry : bond 0.00324 ( 3175) covalent geometry : angle 0.47649 ( 4324) hydrogen bonds : bond 0.04411 ( 257) hydrogen bonds : angle 4.61387 ( 771) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 51 time to evaluate : 0.114 Fit side-chains REVERT: B 251 GLU cc_start: 0.8028 (OUTLIER) cc_final: 0.7356 (mp0) REVERT: B 253 GLU cc_start: 0.8072 (mt-10) cc_final: 0.7579 (mm-30) REVERT: B 291 GLU cc_start: 0.7876 (pt0) cc_final: 0.7659 (pt0) REVERT: B 331 LYS cc_start: 0.8617 (OUTLIER) cc_final: 0.7764 (mtmm) REVERT: B 366 GLU cc_start: 0.8016 (mt-10) cc_final: 0.7770 (mt-10) outliers start: 13 outliers final: 5 residues processed: 57 average time/residue: 0.4790 time to fit residues: 28.1806 Evaluate side-chains 55 residues out of total 329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 48 time to evaluate : 0.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 194 SER Chi-restraints excluded: chain B residue 251 GLU Chi-restraints excluded: chain B residue 331 LYS Chi-restraints excluded: chain B residue 372 LYS Chi-restraints excluded: chain B residue 384 THR Chi-restraints excluded: chain B residue 438 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 18 optimal weight: 0.9990 chunk 37 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 chunk 27 optimal weight: 0.6980 chunk 36 optimal weight: 2.9990 chunk 40 optimal weight: 0.5980 chunk 35 optimal weight: 2.9990 chunk 3 optimal weight: 6.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 224 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.145272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.111153 restraints weight = 3674.255| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 1.78 r_work: 0.3244 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3136 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.1897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3175 Z= 0.143 Angle : 0.477 5.029 4324 Z= 0.245 Chirality : 0.038 0.137 542 Planarity : 0.004 0.040 535 Dihedral : 3.256 13.711 440 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 3.95 % Allowed : 14.89 % Favored : 81.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.47 (0.42), residues: 413 helix: 2.22 (0.28), residues: 332 sheet: -0.72 (1.17), residues: 20 loop : -0.82 (0.80), residues: 61 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 301 TYR 0.009 0.002 TYR B 208 PHE 0.011 0.001 PHE B 237 TRP 0.013 0.001 TRP B 338 HIS 0.001 0.000 HIS B 373 Details of bonding type rmsd covalent geometry : bond 0.00334 ( 3175) covalent geometry : angle 0.47713 ( 4324) hydrogen bonds : bond 0.04269 ( 257) hydrogen bonds : angle 4.52586 ( 771) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 52 time to evaluate : 0.127 Fit side-chains REVERT: B 251 GLU cc_start: 0.8060 (OUTLIER) cc_final: 0.7444 (mp0) REVERT: B 475 ASP cc_start: 0.7574 (m-30) cc_final: 0.7276 (m-30) outliers start: 13 outliers final: 6 residues processed: 58 average time/residue: 0.4531 time to fit residues: 27.1993 Evaluate side-chains 54 residues out of total 329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 47 time to evaluate : 0.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 194 SER Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 251 GLU Chi-restraints excluded: chain B residue 372 LYS Chi-restraints excluded: chain B residue 384 THR Chi-restraints excluded: chain B residue 438 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 1 optimal weight: 0.9980 chunk 38 optimal weight: 0.8980 chunk 2 optimal weight: 0.8980 chunk 25 optimal weight: 0.7980 chunk 8 optimal weight: 0.9980 chunk 3 optimal weight: 5.9990 chunk 12 optimal weight: 0.7980 chunk 36 optimal weight: 8.9990 chunk 24 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 224 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.144326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.110246 restraints weight = 3677.755| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 1.79 r_work: 0.3242 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3135 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.1946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3175 Z= 0.147 Angle : 0.477 5.043 4324 Z= 0.244 Chirality : 0.038 0.140 542 Planarity : 0.004 0.039 535 Dihedral : 3.270 14.080 440 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 4.26 % Allowed : 15.50 % Favored : 80.24 % 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: 2.48 (0.41), residues: 413 helix: 2.24 (0.28), residues: 332 sheet: -0.53 (1.15), residues: 21 loop : -1.01 (0.77), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 301 TYR 0.010 0.002 TYR B 334 PHE 0.011 0.001 PHE B 237 TRP 0.013 0.002 TRP B 338 HIS 0.001 0.000 HIS B 373 Details of bonding type rmsd covalent geometry : bond 0.00346 ( 3175) covalent geometry : angle 0.47702 ( 4324) hydrogen bonds : bond 0.04251 ( 257) hydrogen bonds : angle 4.51904 ( 771) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 45 time to evaluate : 0.100 Fit side-chains REVERT: B 251 GLU cc_start: 0.8081 (OUTLIER) cc_final: 0.7471 (mp0) REVERT: B 331 LYS cc_start: 0.8639 (OUTLIER) cc_final: 0.7761 (mtmm) outliers start: 14 outliers final: 8 residues processed: 51 average time/residue: 0.4175 time to fit residues: 21.9950 Evaluate side-chains 55 residues out of total 329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 45 time to evaluate : 0.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 194 SER Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 251 GLU Chi-restraints excluded: chain B residue 331 LYS Chi-restraints excluded: chain B residue 372 LYS Chi-restraints excluded: chain B residue 384 THR Chi-restraints excluded: chain B residue 436 VAL Chi-restraints excluded: chain B residue 438 THR Chi-restraints excluded: chain B residue 486 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 4 optimal weight: 0.7980 chunk 22 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 chunk 39 optimal weight: 0.9990 chunk 19 optimal weight: 0.6980 chunk 24 optimal weight: 0.6980 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 224 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.144145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.109824 restraints weight = 3702.729| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 1.83 r_work: 0.3263 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3156 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.2025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3175 Z= 0.143 Angle : 0.475 5.056 4324 Z= 0.242 Chirality : 0.038 0.140 542 Planarity : 0.004 0.039 535 Dihedral : 3.252 14.060 440 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 3.95 % Allowed : 15.50 % Favored : 80.55 % 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: 2.64 (0.41), residues: 413 helix: 2.30 (0.28), residues: 335 sheet: -0.59 (1.16), residues: 21 loop : -0.65 (0.76), residues: 57 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 301 TYR 0.010 0.002 TYR B 334 PHE 0.011 0.001 PHE B 237 TRP 0.011 0.001 TRP B 338 HIS 0.001 0.000 HIS B 373 Details of bonding type rmsd covalent geometry : bond 0.00334 ( 3175) covalent geometry : angle 0.47539 ( 4324) hydrogen bonds : bond 0.04197 ( 257) hydrogen bonds : angle 4.50630 ( 771) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 47 time to evaluate : 0.119 Fit side-chains REVERT: B 251 GLU cc_start: 0.8072 (OUTLIER) cc_final: 0.7433 (mp0) REVERT: B 331 LYS cc_start: 0.8591 (OUTLIER) cc_final: 0.7699 (mtmm) REVERT: B 366 GLU cc_start: 0.8081 (mt-10) cc_final: 0.7849 (mt-10) outliers start: 13 outliers final: 8 residues processed: 54 average time/residue: 0.4540 time to fit residues: 25.3474 Evaluate side-chains 55 residues out of total 329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 45 time to evaluate : 0.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 194 SER Chi-restraints excluded: chain B residue 251 GLU Chi-restraints excluded: chain B residue 331 LYS Chi-restraints excluded: chain B residue 372 LYS Chi-restraints excluded: chain B residue 384 THR Chi-restraints excluded: chain B residue 436 VAL Chi-restraints excluded: chain B residue 438 THR Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 486 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 32 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 15 optimal weight: 0.6980 chunk 6 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 35 optimal weight: 2.9990 chunk 14 optimal weight: 0.6980 chunk 23 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 34 optimal weight: 0.9980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 224 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.144208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.109670 restraints weight = 3758.741| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 1.87 r_work: 0.3220 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3112 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.2033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3175 Z= 0.143 Angle : 0.475 5.024 4324 Z= 0.242 Chirality : 0.038 0.141 542 Planarity : 0.004 0.038 535 Dihedral : 3.257 14.291 440 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 3.95 % Allowed : 15.20 % Favored : 80.85 % 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: 2.68 (0.41), residues: 413 helix: 2.34 (0.28), residues: 335 sheet: -0.65 (1.17), residues: 21 loop : -0.69 (0.74), residues: 57 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 465 TYR 0.010 0.002 TYR B 334 PHE 0.011 0.001 PHE B 237 TRP 0.014 0.002 TRP B 338 HIS 0.001 0.000 HIS B 373 Details of bonding type rmsd covalent geometry : bond 0.00333 ( 3175) covalent geometry : angle 0.47459 ( 4324) hydrogen bonds : bond 0.04180 ( 257) hydrogen bonds : angle 4.49699 ( 771) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 46 time to evaluate : 0.114 Fit side-chains REVERT: B 251 GLU cc_start: 0.8095 (OUTLIER) cc_final: 0.7449 (mp0) REVERT: B 366 GLU cc_start: 0.8095 (mt-10) cc_final: 0.7854 (mt-10) REVERT: B 475 ASP cc_start: 0.7703 (m-30) cc_final: 0.7458 (m-30) outliers start: 13 outliers final: 9 residues processed: 52 average time/residue: 0.4576 time to fit residues: 24.6362 Evaluate side-chains 55 residues out of total 329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 45 time to evaluate : 0.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 194 SER Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 251 GLU Chi-restraints excluded: chain B residue 372 LYS Chi-restraints excluded: chain B residue 384 THR Chi-restraints excluded: chain B residue 436 VAL Chi-restraints excluded: chain B residue 438 THR Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 486 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 13 optimal weight: 0.0470 chunk 3 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 chunk 19 optimal weight: 0.5980 chunk 23 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 21 optimal weight: 0.9980 chunk 12 optimal weight: 0.9990 chunk 15 optimal weight: 0.9980 chunk 9 optimal weight: 0.7980 chunk 17 optimal weight: 0.5980 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 224 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.145651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.111752 restraints weight = 3768.364| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 1.81 r_work: 0.3247 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3140 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.2174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3175 Z= 0.121 Angle : 0.454 4.929 4324 Z= 0.231 Chirality : 0.037 0.136 542 Planarity : 0.004 0.038 535 Dihedral : 3.184 15.048 440 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 3.04 % Allowed : 16.11 % Favored : 80.85 % 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: 2.88 (0.41), residues: 413 helix: 2.46 (0.28), residues: 336 sheet: -0.68 (1.17), residues: 21 loop : -0.59 (0.74), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 465 TYR 0.008 0.002 TYR B 208 PHE 0.009 0.001 PHE B 237 TRP 0.012 0.001 TRP B 338 HIS 0.001 0.000 HIS B 313 Details of bonding type rmsd covalent geometry : bond 0.00271 ( 3175) covalent geometry : angle 0.45369 ( 4324) hydrogen bonds : bond 0.03925 ( 257) hydrogen bonds : angle 4.40189 ( 771) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 49 time to evaluate : 0.120 Fit side-chains REVERT: B 251 GLU cc_start: 0.8019 (OUTLIER) cc_final: 0.7456 (mp0) REVERT: B 366 GLU cc_start: 0.8128 (mt-10) cc_final: 0.7910 (mt-10) REVERT: B 475 ASP cc_start: 0.7676 (m-30) cc_final: 0.7439 (m-30) outliers start: 10 outliers final: 7 residues processed: 54 average time/residue: 0.4295 time to fit residues: 23.9446 Evaluate side-chains 55 residues out of total 329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 47 time to evaluate : 0.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 251 GLU Chi-restraints excluded: chain B residue 372 LYS Chi-restraints excluded: chain B residue 384 THR Chi-restraints excluded: chain B residue 436 VAL Chi-restraints excluded: chain B residue 438 THR Chi-restraints excluded: chain B residue 486 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 27 optimal weight: 0.7980 chunk 25 optimal weight: 0.9980 chunk 37 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 10 optimal weight: 0.0010 chunk 18 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 13 optimal weight: 0.0030 chunk 35 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 overall best weight: 0.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 224 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.146507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.112810 restraints weight = 3712.264| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 1.79 r_work: 0.3310 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3206 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.2266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3175 Z= 0.114 Angle : 0.449 4.916 4324 Z= 0.228 Chirality : 0.037 0.135 542 Planarity : 0.004 0.038 535 Dihedral : 3.153 15.413 440 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 3.04 % Allowed : 17.02 % Favored : 79.94 % 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: 2.96 (0.41), residues: 413 helix: 2.54 (0.28), residues: 336 sheet: -0.73 (1.18), residues: 21 loop : -0.64 (0.73), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 465 TYR 0.008 0.001 TYR B 208 PHE 0.009 0.001 PHE B 237 TRP 0.016 0.002 TRP B 338 HIS 0.000 0.000 HIS B 313 Details of bonding type rmsd covalent geometry : bond 0.00252 ( 3175) covalent geometry : angle 0.44861 ( 4324) hydrogen bonds : bond 0.03815 ( 257) hydrogen bonds : angle 4.35249 ( 771) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 48 time to evaluate : 0.135 Fit side-chains REVERT: B 251 GLU cc_start: 0.7979 (OUTLIER) cc_final: 0.7444 (mp0) REVERT: B 475 ASP cc_start: 0.7583 (m-30) cc_final: 0.7341 (m-30) outliers start: 10 outliers final: 8 residues processed: 52 average time/residue: 0.4492 time to fit residues: 24.1911 Evaluate side-chains 53 residues out of total 329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 44 time to evaluate : 0.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 251 GLU Chi-restraints excluded: chain B residue 372 LYS Chi-restraints excluded: chain B residue 384 THR Chi-restraints excluded: chain B residue 436 VAL Chi-restraints excluded: chain B residue 438 THR Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 486 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 8 optimal weight: 0.6980 chunk 31 optimal weight: 0.5980 chunk 39 optimal weight: 0.9990 chunk 14 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.2980 chunk 27 optimal weight: 0.6980 chunk 30 optimal weight: 6.9990 chunk 25 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 18 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 224 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.145968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.112330 restraints weight = 3664.925| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 1.78 r_work: 0.3267 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3159 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.2259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3175 Z= 0.123 Angle : 0.455 4.945 4324 Z= 0.231 Chirality : 0.037 0.137 542 Planarity : 0.004 0.038 535 Dihedral : 3.158 15.074 440 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 3.04 % Allowed : 17.63 % Favored : 79.33 % 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: 2.90 (0.41), residues: 413 helix: 2.50 (0.28), residues: 336 sheet: -0.80 (1.18), residues: 21 loop : -0.66 (0.73), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 465 TYR 0.008 0.002 TYR B 334 PHE 0.009 0.001 PHE B 237 TRP 0.019 0.002 TRP B 338 HIS 0.000 0.000 HIS B 313 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 3175) covalent geometry : angle 0.45520 ( 4324) hydrogen bonds : bond 0.03916 ( 257) hydrogen bonds : angle 4.37059 ( 771) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 46 time to evaluate : 0.152 Fit side-chains REVERT: B 251 GLU cc_start: 0.8009 (OUTLIER) cc_final: 0.7482 (mp0) outliers start: 10 outliers final: 6 residues processed: 51 average time/residue: 0.4724 time to fit residues: 24.8332 Evaluate side-chains 51 residues out of total 329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 44 time to evaluate : 0.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 251 GLU Chi-restraints excluded: chain B residue 372 LYS Chi-restraints excluded: chain B residue 384 THR Chi-restraints excluded: chain B residue 436 VAL Chi-restraints excluded: chain B residue 438 THR Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 486 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 20 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 39 optimal weight: 4.9990 chunk 33 optimal weight: 0.9980 chunk 16 optimal weight: 0.7980 chunk 6 optimal weight: 0.8980 chunk 7 optimal weight: 0.5980 chunk 2 optimal weight: 0.9990 chunk 19 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 224 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.145214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.111403 restraints weight = 3711.760| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 1.81 r_work: 0.3250 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3143 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.2252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3175 Z= 0.133 Angle : 0.467 5.121 4324 Z= 0.238 Chirality : 0.038 0.137 542 Planarity : 0.004 0.038 535 Dihedral : 3.197 15.003 440 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 2.74 % Allowed : 17.93 % Favored : 79.33 % 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: 2.82 (0.41), residues: 413 helix: 2.43 (0.28), residues: 336 sheet: -0.86 (1.18), residues: 21 loop : -0.63 (0.72), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 465 TYR 0.009 0.002 TYR B 334 PHE 0.010 0.001 PHE B 237 TRP 0.019 0.002 TRP B 338 HIS 0.000 0.000 HIS B 316 Details of bonding type rmsd covalent geometry : bond 0.00307 ( 3175) covalent geometry : angle 0.46744 ( 4324) hydrogen bonds : bond 0.04022 ( 257) hydrogen bonds : angle 4.40452 ( 771) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1248.64 seconds wall clock time: 22 minutes 0.11 seconds (1320.11 seconds total)