Starting phenix.real_space_refine on Tue Mar 3 12:17:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7uv0_26808/03_2026/7uv0_26808.cif Found real_map, /net/cci-nas-00/data/ceres_data/7uv0_26808/03_2026/7uv0_26808.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7uv0_26808/03_2026/7uv0_26808.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7uv0_26808/03_2026/7uv0_26808.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7uv0_26808/03_2026/7uv0_26808.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7uv0_26808/03_2026/7uv0_26808.map" } resolution = 3.1 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= 0.001 sd= 0.081 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: 7 Type Number sf(0) Gaussians I 1 10.91 5 P 1 5.49 5 S 27 5.16 5 Na 2 4.78 5 C 2494 2.51 5 N 594 2.21 5 O 665 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model 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: 3784 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3739 Number of conformers: 1 Conformer: "" Number of residues, atoms: 501, 3739 Classifications: {'peptide': 501} Link IDs: {'PTRANS': 24, 'TRANS': 476} Chain breaks: 3 Chain: "A" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 45 Unusual residues: {' NA': 2, '3PH': 1, 'IOD': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 Time building chain proxies: 1.06, per 1000 atoms: 0.28 Number of scatterers: 3784 At special positions: 0 Unit cell: (67.284, 85.44, 83.304, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) I 1 52.95 S 27 16.00 P 1 15.00 Na 2 11.00 O 665 8.00 N 594 7.00 C 2494 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 310 " - pdb=" SG CYS A 483 " distance=2.03 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: 0.37 Conformation dependent library (CDL) restraints added in 149.6 milliseconds 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 892 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 0 sheets defined 78.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.15 Creating SS restraints... Processing helix chain 'A' and resid 13 through 36 removed outlier: 3.765A pdb=" N TYR A 17 " --> pdb=" O GLY A 13 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLY A 18 " --> pdb=" O ALA A 14 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL A 19 " --> pdb=" O TRP A 15 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 67 removed outlier: 3.647A pdb=" N ALA A 64 " --> pdb=" O GLY A 60 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N PHE A 67 " --> pdb=" O LEU A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 84 Proline residue: A 77 - end of helix Processing helix chain 'A' and resid 85 through 87 No H-bonds generated for 'chain 'A' and resid 85 through 87' Processing helix chain 'A' and resid 88 through 104 removed outlier: 3.835A pdb=" N ALA A 92 " --> pdb=" O LEU A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 112 Processing helix chain 'A' and resid 118 through 125 Processing helix chain 'A' and resid 126 through 161 Proline residue: A 152 - end of helix removed outlier: 3.511A pdb=" N GLY A 161 " --> pdb=" O ASN A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 180 Processing helix chain 'A' and resid 191 through 213 Processing helix chain 'A' and resid 215 through 226 removed outlier: 3.502A pdb=" N HIS A 226 " --> pdb=" O LEU A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 260 removed outlier: 4.197A pdb=" N THR A 252 " --> pdb=" O ILE A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 271 Processing helix chain 'A' and resid 275 through 307 removed outlier: 3.603A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE A 301 " --> pdb=" O ALA A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 316 removed outlier: 3.546A pdb=" N GLY A 316 " --> pdb=" O LEU A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 333 Processing helix chain 'A' and resid 338 through 370 removed outlier: 4.119A pdb=" N THR A 351 " --> pdb=" O ALA A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 409 removed outlier: 3.543A pdb=" N VAL A 384 " --> pdb=" O PRO A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 437 Proline residue: A 426 - end of helix Processing helix chain 'A' and resid 441 through 466 removed outlier: 3.740A pdb=" N THR A 464 " --> pdb=" O ALA A 460 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N TYR A 466 " --> pdb=" O GLY A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 546 removed outlier: 4.345A pdb=" N ALA A 528 " --> pdb=" O LEU A 524 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N THR A 533 " --> pdb=" O LEU A 529 " (cutoff:3.500A) 283 hydrogen bonds defined for protein. 846 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: 0.62 Time building geometry restraints manager: 0.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 638 1.33 - 1.45: 1013 1.45 - 1.57: 2172 1.57 - 1.70: 2 1.70 - 1.82: 42 Bond restraints: 3867 Sorted by residual: bond pdb=" O13 3PH A 704 " pdb=" P 3PH A 704 " ideal model delta sigma weight residual 1.522 1.654 -0.132 2.00e-02 2.50e+03 4.36e+01 bond pdb=" O11 3PH A 704 " pdb=" P 3PH A 704 " ideal model delta sigma weight residual 1.703 1.644 0.059 2.00e-02 2.50e+03 8.84e+00 bond pdb=" O12 3PH A 704 " pdb=" P 3PH A 704 " ideal model delta sigma weight residual 1.526 1.490 0.036 2.00e-02 2.50e+03 3.25e+00 bond pdb=" O14 3PH A 704 " pdb=" P 3PH A 704 " ideal model delta sigma weight residual 1.527 1.493 0.034 2.00e-02 2.50e+03 2.97e+00 bond pdb=" C1 3PH A 704 " pdb=" O11 3PH A 704 " ideal model delta sigma weight residual 1.385 1.410 -0.025 2.00e-02 2.50e+03 1.50e+00 ... (remaining 3862 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.01: 5197 2.01 - 4.01: 64 4.01 - 6.02: 9 6.02 - 8.03: 0 8.03 - 10.04: 2 Bond angle restraints: 5272 Sorted by residual: angle pdb=" O12 3PH A 704 " pdb=" P 3PH A 704 " pdb=" O14 3PH A 704 " ideal model delta sigma weight residual 113.84 123.88 -10.04 3.00e+00 1.11e-01 1.12e+01 angle pdb=" O13 3PH A 704 " pdb=" P 3PH A 704 " pdb=" O14 3PH A 704 " ideal model delta sigma weight residual 115.01 104.99 10.02 3.00e+00 1.11e-01 1.12e+01 angle pdb=" CA PRO A 512 " pdb=" C PRO A 512 " pdb=" N ALA A 513 " ideal model delta sigma weight residual 114.74 117.04 -2.30 1.03e+00 9.43e-01 4.97e+00 angle pdb=" O12 3PH A 704 " pdb=" P 3PH A 704 " pdb=" O13 3PH A 704 " ideal model delta sigma weight residual 115.12 109.29 5.83 3.00e+00 1.11e-01 3.78e+00 angle pdb=" O11 3PH A 704 " pdb=" P 3PH A 704 " pdb=" O14 3PH A 704 " ideal model delta sigma weight residual 104.78 110.05 -5.27 3.00e+00 1.11e-01 3.08e+00 ... (remaining 5267 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.89: 2016 15.89 - 31.78: 172 31.78 - 47.66: 33 47.66 - 63.55: 17 63.55 - 79.44: 3 Dihedral angle restraints: 2241 sinusoidal: 829 harmonic: 1412 Sorted by residual: dihedral pdb=" CA ASP A 309 " pdb=" C ASP A 309 " pdb=" N CYS A 310 " pdb=" CA CYS A 310 " ideal model delta harmonic sigma weight residual 180.00 -164.24 -15.76 0 5.00e+00 4.00e-02 9.93e+00 dihedral pdb=" CA HIS A 273 " pdb=" C HIS A 273 " pdb=" N THR A 274 " pdb=" CA THR A 274 " ideal model delta harmonic sigma weight residual 180.00 164.58 15.42 0 5.00e+00 4.00e-02 9.51e+00 dihedral pdb=" CA LEU A 436 " pdb=" CB LEU A 436 " pdb=" CG LEU A 436 " pdb=" CD1 LEU A 436 " ideal model delta sinusoidal sigma weight residual 60.00 117.14 -57.14 3 1.50e+01 4.44e-03 9.43e+00 ... (remaining 2238 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 471 0.039 - 0.079: 137 0.079 - 0.118: 24 0.118 - 0.158: 1 0.158 - 0.197: 1 Chirality restraints: 634 Sorted by residual: chirality pdb=" C2 3PH A 704 " pdb=" C1 3PH A 704 " pdb=" C3 3PH A 704 " pdb=" O21 3PH A 704 " both_signs ideal model delta sigma weight residual False -2.33 -2.52 0.20 2.00e-01 2.50e+01 9.74e-01 chirality pdb=" CA ILE A 229 " pdb=" N ILE A 229 " pdb=" C ILE A 229 " pdb=" CB ILE A 229 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.87e-01 chirality pdb=" CA PRO A 337 " pdb=" N PRO A 337 " pdb=" C PRO A 337 " pdb=" CB PRO A 337 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.41e-01 ... (remaining 631 not shown) Planarity restraints: 639 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 57 " 0.036 5.00e-02 4.00e+02 5.50e-02 4.83e+00 pdb=" N PRO A 58 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO A 58 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 58 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 372 " 0.033 5.00e-02 4.00e+02 4.92e-02 3.88e+00 pdb=" N PRO A 373 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO A 373 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 373 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 247 " 0.008 2.00e-02 2.50e+03 1.59e-02 2.54e+00 pdb=" C PHE A 247 " -0.028 2.00e-02 2.50e+03 pdb=" O PHE A 247 " 0.010 2.00e-02 2.50e+03 pdb=" N ILE A 248 " 0.009 2.00e-02 2.50e+03 ... (remaining 636 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.72: 191 2.72 - 3.28: 4322 3.28 - 3.84: 6823 3.84 - 4.40: 8257 4.40 - 4.96: 14074 Nonbonded interactions: 33667 Sorted by model distance: nonbonded pdb=" O PHE A 125 " pdb=" OG SER A 126 " model vdw 2.160 3.040 nonbonded pdb=" OE1 GLN A 72 " pdb="NA NA A 702 " model vdw 2.201 2.470 nonbonded pdb=" OH TYR A 17 " pdb=" O THR A 160 " model vdw 2.261 3.040 nonbonded pdb=" O GLN A 414 " pdb=" OG1 THR A 418 " model vdw 2.338 3.040 nonbonded pdb=" O THR A 115 " pdb=" NE2 GLN A 267 " model vdw 2.343 3.120 ... (remaining 33662 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: 0.810 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: 0.050 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.820 Find NCS groups from input model: 0.020 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:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.132 3868 Z= 0.226 Angle : 0.611 10.036 5274 Z= 0.307 Chirality : 0.037 0.197 634 Planarity : 0.005 0.055 639 Dihedral : 13.420 79.437 1346 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.71 % Favored : 92.29 % Rotamer: Outliers : 0.51 % Allowed : 8.86 % Favored : 90.63 % 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 are not related in a simple way. whole: 0.23 (0.40), residues: 493 helix: 0.93 (0.28), residues: 377 sheet: None (None), residues: 0 loop : -2.40 (0.61), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 381 TYR 0.008 0.001 TYR A 348 PHE 0.009 0.001 PHE A 304 TRP 0.012 0.001 TRP A 165 HIS 0.002 0.001 HIS A 226 Details of bonding type rmsd covalent geometry : bond 0.00495 ( 3867) covalent geometry : angle 0.61082 ( 5272) SS BOND : bond 0.00173 ( 1) SS BOND : angle 1.33499 ( 2) hydrogen bonds : bond 0.13769 ( 283) hydrogen bonds : angle 6.48125 ( 846) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 62 time to evaluate : 0.129 Fit side-chains REVERT: A 154 LEU cc_start: 0.8449 (OUTLIER) cc_final: 0.8196 (mt) REVERT: A 232 MET cc_start: 0.7860 (mmt) cc_final: 0.7589 (mmm) REVERT: A 269 TYR cc_start: 0.6460 (m-10) cc_final: 0.6194 (m-10) outliers start: 2 outliers final: 0 residues processed: 64 average time/residue: 0.0624 time to fit residues: 5.1341 Evaluate side-chains 57 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 56 time to evaluate : 0.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 24 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 chunk 26 optimal weight: 0.9990 chunk 2 optimal weight: 3.9990 chunk 16 optimal weight: 0.6980 chunk 32 optimal weight: 2.9990 chunk 31 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 chunk 22 optimal weight: 0.7980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 218 ASN A 265 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.152215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.131452 restraints weight = 3347.510| |-----------------------------------------------------------------------------| r_work (start): 0.3616 rms_B_bonded: 1.22 r_work: 0.3533 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3414 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7430 moved from start: 0.1052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 3868 Z= 0.199 Angle : 0.635 9.135 5274 Z= 0.318 Chirality : 0.040 0.142 634 Planarity : 0.005 0.058 639 Dihedral : 9.564 60.329 576 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 2.78 % Allowed : 11.39 % Favored : 85.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.98 (0.41), residues: 493 helix: 1.41 (0.28), residues: 383 sheet: None (None), residues: 0 loop : -2.05 (0.66), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 268 TYR 0.014 0.002 TYR A 118 PHE 0.014 0.002 PHE A 12 TRP 0.014 0.002 TRP A 165 HIS 0.003 0.001 HIS A 226 Details of bonding type rmsd covalent geometry : bond 0.00476 ( 3867) covalent geometry : angle 0.63450 ( 5272) SS BOND : bond 0.00086 ( 1) SS BOND : angle 1.23645 ( 2) hydrogen bonds : bond 0.04206 ( 283) hydrogen bonds : angle 4.72750 ( 846) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 65 time to evaluate : 0.133 Fit side-chains REVERT: A 68 MET cc_start: 0.6847 (tmt) cc_final: 0.6461 (tmm) REVERT: A 154 LEU cc_start: 0.8395 (OUTLIER) cc_final: 0.8040 (tt) REVERT: A 269 TYR cc_start: 0.6378 (m-10) cc_final: 0.6142 (m-10) outliers start: 11 outliers final: 5 residues processed: 72 average time/residue: 0.0611 time to fit residues: 5.6571 Evaluate side-chains 64 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 58 time to evaluate : 0.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 285 ASN Chi-restraints excluded: chain A residue 310 CYS Chi-restraints excluded: chain A residue 342 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 12 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 6 optimal weight: 0.3980 chunk 28 optimal weight: 0.1980 chunk 41 optimal weight: 2.9990 chunk 40 optimal weight: 0.6980 chunk 17 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 49 optimal weight: 0.3980 chunk 5 optimal weight: 0.8980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 218 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.160927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.140436 restraints weight = 3946.160| |-----------------------------------------------------------------------------| r_work (start): 0.3642 rms_B_bonded: 1.33 r_work: 0.3556 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3437 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7430 moved from start: 0.1429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3868 Z= 0.141 Angle : 0.567 8.796 5274 Z= 0.288 Chirality : 0.038 0.148 634 Planarity : 0.005 0.057 639 Dihedral : 8.887 62.721 576 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 2.78 % Allowed : 13.42 % Favored : 83.80 % 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 are not related in a simple way. whole: 1.37 (0.41), residues: 493 helix: 1.68 (0.28), residues: 386 sheet: None (None), residues: 0 loop : -2.00 (0.66), residues: 107 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 268 TYR 0.012 0.001 TYR A 118 PHE 0.016 0.002 PHE A 12 TRP 0.013 0.001 TRP A 165 HIS 0.002 0.001 HIS A 226 Details of bonding type rmsd covalent geometry : bond 0.00327 ( 3867) covalent geometry : angle 0.56679 ( 5272) SS BOND : bond 0.00031 ( 1) SS BOND : angle 0.93955 ( 2) hydrogen bonds : bond 0.03614 ( 283) hydrogen bonds : angle 4.30435 ( 846) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 60 time to evaluate : 0.144 Fit side-chains REVERT: A 154 LEU cc_start: 0.8434 (OUTLIER) cc_final: 0.8217 (tt) outliers start: 11 outliers final: 5 residues processed: 67 average time/residue: 0.0611 time to fit residues: 5.2784 Evaluate side-chains 62 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 56 time to evaluate : 0.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 ASN Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 285 ASN Chi-restraints excluded: chain A residue 310 CYS Chi-restraints excluded: chain A residue 342 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 46 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 9 optimal weight: 0.2980 chunk 34 optimal weight: 0.9990 chunk 17 optimal weight: 0.5980 chunk 3 optimal weight: 0.8980 chunk 4 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.153795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.133201 restraints weight = 3339.971| |-----------------------------------------------------------------------------| r_work (start): 0.3549 rms_B_bonded: 1.21 r_work: 0.3466 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3348 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7328 moved from start: 0.1592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 3868 Z= 0.160 Angle : 0.579 8.526 5274 Z= 0.291 Chirality : 0.039 0.162 634 Planarity : 0.005 0.059 639 Dihedral : 8.403 65.418 576 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 4.05 % Allowed : 13.67 % Favored : 82.28 % 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 are not related in a simple way. whole: 1.32 (0.41), residues: 493 helix: 1.59 (0.28), residues: 387 sheet: None (None), residues: 0 loop : -1.84 (0.66), residues: 106 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 268 TYR 0.010 0.001 TYR A 120 PHE 0.014 0.002 PHE A 304 TRP 0.013 0.001 TRP A 165 HIS 0.001 0.000 HIS A 226 Details of bonding type rmsd covalent geometry : bond 0.00381 ( 3867) covalent geometry : angle 0.57843 ( 5272) SS BOND : bond 0.00438 ( 1) SS BOND : angle 1.09856 ( 2) hydrogen bonds : bond 0.03558 ( 283) hydrogen bonds : angle 4.24172 ( 846) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 63 time to evaluate : 0.138 Fit side-chains REVERT: A 206 LEU cc_start: 0.7405 (OUTLIER) cc_final: 0.7164 (tp) REVERT: A 269 TYR cc_start: 0.6423 (m-10) cc_final: 0.6222 (m-10) outliers start: 16 outliers final: 10 residues processed: 73 average time/residue: 0.0698 time to fit residues: 6.4689 Evaluate side-chains 69 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 58 time to evaluate : 0.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 ASN Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 285 ASN Chi-restraints excluded: chain A residue 310 CYS Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 375 MET Chi-restraints excluded: chain A residue 435 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 17 optimal weight: 0.7980 chunk 0 optimal weight: 1.9990 chunk 1 optimal weight: 0.6980 chunk 5 optimal weight: 0.4980 chunk 19 optimal weight: 0.8980 chunk 16 optimal weight: 0.6980 chunk 42 optimal weight: 0.5980 chunk 20 optimal weight: 0.3980 chunk 27 optimal weight: 0.1980 chunk 26 optimal weight: 0.5980 chunk 8 optimal weight: 2.9990 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.155956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.135083 restraints weight = 3318.291| |-----------------------------------------------------------------------------| r_work (start): 0.3574 rms_B_bonded: 1.25 r_work: 0.3488 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3370 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7320 moved from start: 0.1820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3868 Z= 0.131 Angle : 0.559 8.634 5274 Z= 0.279 Chirality : 0.037 0.144 634 Planarity : 0.004 0.058 639 Dihedral : 7.739 68.447 574 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 3.04 % Allowed : 15.44 % Favored : 81.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.56 (0.41), residues: 493 helix: 1.74 (0.28), residues: 388 sheet: None (None), residues: 0 loop : -1.69 (0.67), residues: 105 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 268 TYR 0.008 0.001 TYR A 120 PHE 0.019 0.002 PHE A 12 TRP 0.012 0.001 TRP A 165 HIS 0.001 0.000 HIS A 226 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 3867) covalent geometry : angle 0.55901 ( 5272) SS BOND : bond 0.00115 ( 1) SS BOND : angle 0.73562 ( 2) hydrogen bonds : bond 0.03268 ( 283) hydrogen bonds : angle 4.05207 ( 846) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 60 time to evaluate : 0.144 Fit side-chains REVERT: A 15 TRP cc_start: 0.6312 (m-90) cc_final: 0.5543 (m100) outliers start: 12 outliers final: 9 residues processed: 68 average time/residue: 0.0655 time to fit residues: 5.6737 Evaluate side-chains 66 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 57 time to evaluate : 0.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 ASN Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 178 TYR Chi-restraints excluded: chain A residue 285 ASN Chi-restraints excluded: chain A residue 310 CYS Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 375 MET Chi-restraints excluded: chain A residue 435 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 0 optimal weight: 2.9990 chunk 26 optimal weight: 0.6980 chunk 25 optimal weight: 0.9980 chunk 30 optimal weight: 0.7980 chunk 10 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 chunk 27 optimal weight: 0.5980 chunk 40 optimal weight: 0.3980 chunk 9 optimal weight: 0.5980 chunk 39 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.155277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.134060 restraints weight = 3445.546| |-----------------------------------------------------------------------------| r_work (start): 0.3582 rms_B_bonded: 1.28 r_work: 0.3497 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3379 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7344 moved from start: 0.1894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3868 Z= 0.147 Angle : 0.588 10.801 5274 Z= 0.288 Chirality : 0.038 0.143 634 Planarity : 0.004 0.058 639 Dihedral : 7.610 70.152 574 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 3.54 % Allowed : 15.95 % Favored : 80.51 % 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 are not related in a simple way. whole: 1.53 (0.41), residues: 493 helix: 1.70 (0.28), residues: 388 sheet: None (None), residues: 0 loop : -1.60 (0.67), residues: 105 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 268 TYR 0.008 0.001 TYR A 120 PHE 0.013 0.002 PHE A 304 TRP 0.012 0.001 TRP A 165 HIS 0.001 0.000 HIS A 226 Details of bonding type rmsd covalent geometry : bond 0.00350 ( 3867) covalent geometry : angle 0.58787 ( 5272) SS BOND : bond 0.00280 ( 1) SS BOND : angle 1.13799 ( 2) hydrogen bonds : bond 0.03317 ( 283) hydrogen bonds : angle 4.06723 ( 846) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 59 time to evaluate : 0.149 Fit side-chains REVERT: A 15 TRP cc_start: 0.6365 (m-90) cc_final: 0.5593 (m100) REVERT: A 268 ARG cc_start: 0.7628 (mtt90) cc_final: 0.7095 (mpp80) outliers start: 14 outliers final: 11 residues processed: 68 average time/residue: 0.0680 time to fit residues: 5.8733 Evaluate side-chains 69 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 58 time to evaluate : 0.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 ASN Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 178 TYR Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 285 ASN Chi-restraints excluded: chain A residue 310 CYS Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 375 MET Chi-restraints excluded: chain A residue 435 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 13 optimal weight: 0.6980 chunk 47 optimal weight: 0.6980 chunk 39 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 8 optimal weight: 0.9990 chunk 32 optimal weight: 0.8980 chunk 24 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 chunk 27 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.154403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.133128 restraints weight = 3396.282| |-----------------------------------------------------------------------------| r_work (start): 0.3592 rms_B_bonded: 1.26 r_work: 0.3508 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3391 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7399 moved from start: 0.1911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 3868 Z= 0.166 Angle : 0.621 11.742 5274 Z= 0.303 Chirality : 0.039 0.143 634 Planarity : 0.005 0.058 639 Dihedral : 7.561 71.678 574 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 3.54 % Allowed : 16.46 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.40 (0.41), residues: 493 helix: 1.60 (0.28), residues: 387 sheet: None (None), residues: 0 loop : -1.60 (0.67), residues: 106 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 268 TYR 0.010 0.001 TYR A 269 PHE 0.013 0.002 PHE A 304 TRP 0.012 0.001 TRP A 165 HIS 0.001 0.000 HIS A 226 Details of bonding type rmsd covalent geometry : bond 0.00401 ( 3867) covalent geometry : angle 0.62111 ( 5272) SS BOND : bond 0.00267 ( 1) SS BOND : angle 0.93045 ( 2) hydrogen bonds : bond 0.03418 ( 283) hydrogen bonds : angle 4.13774 ( 846) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 57 time to evaluate : 0.103 Fit side-chains REVERT: A 15 TRP cc_start: 0.6386 (m-90) cc_final: 0.5615 (m100) REVERT: A 268 ARG cc_start: 0.7745 (mtt90) cc_final: 0.7232 (mpp80) outliers start: 14 outliers final: 11 residues processed: 67 average time/residue: 0.0592 time to fit residues: 5.0403 Evaluate side-chains 68 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 57 time to evaluate : 0.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 ASN Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 178 TYR Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 285 ASN Chi-restraints excluded: chain A residue 310 CYS Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 375 MET Chi-restraints excluded: chain A residue 435 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 32 optimal weight: 0.9980 chunk 28 optimal weight: 3.9990 chunk 12 optimal weight: 0.1980 chunk 35 optimal weight: 0.4980 chunk 42 optimal weight: 0.7980 chunk 44 optimal weight: 0.3980 chunk 39 optimal weight: 1.9990 chunk 14 optimal weight: 0.6980 chunk 23 optimal weight: 5.9990 chunk 2 optimal weight: 0.1980 chunk 22 optimal weight: 0.6980 overall best weight: 0.3980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.163897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.144052 restraints weight = 3213.953| |-----------------------------------------------------------------------------| r_work (start): 0.3603 rms_B_bonded: 1.16 r_work: 0.3515 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3402 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7308 moved from start: 0.2101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3868 Z= 0.129 Angle : 0.577 10.829 5274 Z= 0.284 Chirality : 0.037 0.165 634 Planarity : 0.004 0.057 639 Dihedral : 7.395 74.253 574 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 2.53 % Allowed : 17.22 % Favored : 80.25 % 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 are not related in a simple way. whole: 1.68 (0.41), residues: 493 helix: 1.78 (0.28), residues: 388 sheet: None (None), residues: 0 loop : -1.45 (0.68), residues: 105 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 268 TYR 0.012 0.001 TYR A 269 PHE 0.020 0.002 PHE A 12 TRP 0.011 0.001 TRP A 165 HIS 0.002 0.001 HIS A 273 Details of bonding type rmsd covalent geometry : bond 0.00295 ( 3867) covalent geometry : angle 0.57748 ( 5272) SS BOND : bond 0.00256 ( 1) SS BOND : angle 0.57480 ( 2) hydrogen bonds : bond 0.03156 ( 283) hydrogen bonds : angle 3.95660 ( 846) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 62 time to evaluate : 0.129 Fit side-chains REVERT: A 15 TRP cc_start: 0.6343 (m-90) cc_final: 0.5517 (m100) REVERT: A 268 ARG cc_start: 0.7704 (mtt90) cc_final: 0.7219 (mpp80) outliers start: 10 outliers final: 8 residues processed: 68 average time/residue: 0.0634 time to fit residues: 5.3701 Evaluate side-chains 66 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 58 time to evaluate : 0.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 ASN Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 178 TYR Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 285 ASN Chi-restraints excluded: chain A residue 310 CYS Chi-restraints excluded: chain A residue 375 MET Chi-restraints excluded: chain A residue 435 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 4 optimal weight: 0.7980 chunk 40 optimal weight: 0.8980 chunk 7 optimal weight: 0.9980 chunk 10 optimal weight: 0.7980 chunk 36 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 chunk 48 optimal weight: 0.3980 chunk 2 optimal weight: 4.9990 chunk 22 optimal weight: 0.6980 chunk 46 optimal weight: 0.0170 chunk 13 optimal weight: 0.7980 overall best weight: 0.5418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.156212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.135100 restraints weight = 3347.024| |-----------------------------------------------------------------------------| r_work (start): 0.3585 rms_B_bonded: 1.25 r_work: 0.3499 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3382 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7332 moved from start: 0.2114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3868 Z= 0.144 Angle : 0.607 13.668 5274 Z= 0.295 Chirality : 0.038 0.163 634 Planarity : 0.005 0.058 639 Dihedral : 7.404 74.539 574 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 2.03 % Allowed : 18.73 % Favored : 79.24 % 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 are not related in a simple way. whole: 1.59 (0.41), residues: 493 helix: 1.72 (0.28), residues: 388 sheet: None (None), residues: 0 loop : -1.52 (0.67), residues: 105 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 82 TYR 0.009 0.001 TYR A 269 PHE 0.016 0.002 PHE A 12 TRP 0.011 0.001 TRP A 165 HIS 0.000 0.000 HIS A 226 Details of bonding type rmsd covalent geometry : bond 0.00341 ( 3867) covalent geometry : angle 0.60716 ( 5272) SS BOND : bond 0.00222 ( 1) SS BOND : angle 0.64293 ( 2) hydrogen bonds : bond 0.03225 ( 283) hydrogen bonds : angle 4.04169 ( 846) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 59 time to evaluate : 0.133 Fit side-chains REVERT: A 15 TRP cc_start: 0.6356 (m-90) cc_final: 0.5506 (m100) REVERT: A 268 ARG cc_start: 0.7710 (mtt90) cc_final: 0.7220 (mpp80) outliers start: 8 outliers final: 8 residues processed: 64 average time/residue: 0.0708 time to fit residues: 5.7626 Evaluate side-chains 67 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 59 time to evaluate : 0.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 ASN Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 178 TYR Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 285 ASN Chi-restraints excluded: chain A residue 310 CYS Chi-restraints excluded: chain A residue 375 MET Chi-restraints excluded: chain A residue 435 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 40 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 39 optimal weight: 0.6980 chunk 0 optimal weight: 1.9990 chunk 12 optimal weight: 0.5980 chunk 16 optimal weight: 0.8980 chunk 1 optimal weight: 0.7980 chunk 18 optimal weight: 0.9980 chunk 6 optimal weight: 0.0670 chunk 27 optimal weight: 0.7980 chunk 9 optimal weight: 0.9980 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.155905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.134483 restraints weight = 3474.780| |-----------------------------------------------------------------------------| r_work (start): 0.3589 rms_B_bonded: 1.29 r_work: 0.3502 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3385 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7342 moved from start: 0.2136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3868 Z= 0.149 Angle : 0.617 14.694 5274 Z= 0.299 Chirality : 0.038 0.161 634 Planarity : 0.005 0.058 639 Dihedral : 7.420 75.634 574 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 2.53 % Allowed : 18.48 % Favored : 78.99 % 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 are not related in a simple way. whole: 1.56 (0.41), residues: 493 helix: 1.70 (0.28), residues: 388 sheet: None (None), residues: 0 loop : -1.49 (0.67), residues: 105 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 82 TYR 0.010 0.001 TYR A 269 PHE 0.023 0.002 PHE A 518 TRP 0.011 0.001 TRP A 165 HIS 0.001 0.000 HIS A 226 Details of bonding type rmsd covalent geometry : bond 0.00353 ( 3867) covalent geometry : angle 0.61659 ( 5272) SS BOND : bond 0.00246 ( 1) SS BOND : angle 0.60001 ( 2) hydrogen bonds : bond 0.03248 ( 283) hydrogen bonds : angle 4.06035 ( 846) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 61 time to evaluate : 0.126 Fit side-chains REVERT: A 15 TRP cc_start: 0.6401 (m-90) cc_final: 0.5525 (m100) outliers start: 10 outliers final: 9 residues processed: 69 average time/residue: 0.0720 time to fit residues: 6.2472 Evaluate side-chains 69 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 60 time to evaluate : 0.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 ASN Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 178 TYR Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 285 ASN Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 375 MET Chi-restraints excluded: chain A residue 435 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 27 optimal weight: 0.9980 chunk 25 optimal weight: 0.6980 chunk 21 optimal weight: 2.9990 chunk 39 optimal weight: 0.5980 chunk 9 optimal weight: 0.3980 chunk 43 optimal weight: 0.0870 chunk 1 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 chunk 45 optimal weight: 0.0670 chunk 37 optimal weight: 1.9990 chunk 41 optimal weight: 0.5980 overall best weight: 0.3496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.158238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.137057 restraints weight = 3411.032| |-----------------------------------------------------------------------------| r_work (start): 0.3609 rms_B_bonded: 1.28 r_work: 0.3521 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3406 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7313 moved from start: 0.2315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3868 Z= 0.125 Angle : 0.595 14.802 5274 Z= 0.289 Chirality : 0.037 0.160 634 Planarity : 0.004 0.057 639 Dihedral : 7.336 77.416 574 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 2.28 % Allowed : 19.49 % Favored : 78.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.76 (0.41), residues: 493 helix: 1.87 (0.28), residues: 388 sheet: None (None), residues: 0 loop : -1.55 (0.67), residues: 105 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 82 TYR 0.013 0.001 TYR A 348 PHE 0.015 0.001 PHE A 12 TRP 0.011 0.001 TRP A 165 HIS 0.000 0.000 HIS A 226 Details of bonding type rmsd covalent geometry : bond 0.00287 ( 3867) covalent geometry : angle 0.59506 ( 5272) SS BOND : bond 0.00208 ( 1) SS BOND : angle 0.45758 ( 2) hydrogen bonds : bond 0.03072 ( 283) hydrogen bonds : angle 3.94077 ( 846) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1176.32 seconds wall clock time: 20 minutes 46.80 seconds (1246.80 seconds total)