Starting phenix.real_space_refine on Tue Mar 3 11:43:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7qes_13939/03_2026/7qes_13939.cif Found real_map, /net/cci-nas-00/data/ceres_data/7qes_13939/03_2026/7qes_13939.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7qes_13939/03_2026/7qes_13939.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7qes_13939/03_2026/7qes_13939.map" model { file = "/net/cci-nas-00/data/ceres_data/7qes_13939/03_2026/7qes_13939.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7qes_13939/03_2026/7qes_13939.cif" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 29 5.16 5 C 2066 2.51 5 N 472 2.21 5 O 509 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3076 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1494 Classifications: {'peptide': 184} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 177} Chain breaks: 1 Chain: "B" Number of atoms: 1483 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1483 Classifications: {'peptide': 182} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 175} Chain breaks: 1 Chain: "A" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 40 Unusual residues: {'LMT': 4, 'PTY': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 159 Unresolved non-hydrogen angles: 214 Unresolved non-hydrogen dihedrals: 264 Unresolved non-hydrogen chiralities: 41 Planarities with less than four sites: {'PTY:plan-1': 1, 'PTY:plan-2': 1} Unresolved non-hydrogen planarities: 6 Chain: "B" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 45 Unusual residues: {'LMT': 4, 'PTY': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 154 Unresolved non-hydrogen angles: 209 Unresolved non-hydrogen dihedrals: 259 Unresolved non-hydrogen chiralities: 41 Planarities with less than four sites: {'PTY:plan-1': 1, 'PTY:plan-2': 1} Unresolved non-hydrogen planarities: 6 Chain: "A" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "B" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Time building chain proxies: 1.00, per 1000 atoms: 0.33 Number of scatterers: 3076 At special positions: 0 Unit cell: (70.85, 66.49, 85.02, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 29 16.00 O 509 8.00 N 472 7.00 C 2066 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 53 " - pdb=" SG CYS A 180 " distance=2.03 Simple disulfide: pdb=" SG CYS A 60 " - pdb=" SG CYS A 174 " distance=2.03 Simple disulfide: pdb=" SG CYS A 64 " - pdb=" SG CYS A 169 " distance=2.03 Simple disulfide: pdb=" SG CYS B 53 " - pdb=" SG CYS B 180 " distance=2.03 Simple disulfide: pdb=" SG CYS B 60 " - pdb=" SG CYS B 174 " distance=2.03 Simple disulfide: pdb=" SG CYS B 64 " - pdb=" SG CYS B 169 " 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: 0.30 Conformation dependent library (CDL) restraints added in 112.9 milliseconds 716 Ramachandran restraints generated. 358 Oldfield, 0 Emsley, 358 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 700 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 2 sheets defined 75.4% alpha, 3.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.05 Creating SS restraints... Processing helix chain 'A' and resid 5 through 15 removed outlier: 3.766A pdb=" N ILE A 9 " --> pdb=" O THR A 5 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LYS A 15 " --> pdb=" O GLY A 11 " (cutoff:3.500A) Processing helix chain 'A' and resid 18 through 39 removed outlier: 3.912A pdb=" N ILE A 23 " --> pdb=" O SER A 19 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N LEU A 25 " --> pdb=" O GLY A 21 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N THR A 26 " --> pdb=" O LYS A 22 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA A 39 " --> pdb=" O ILE A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 40 through 43 Processing helix chain 'A' and resid 59 through 69 Processing helix chain 'A' and resid 72 through 97 Proline residue: A 87 - end of helix Processing helix chain 'A' and resid 132 through 159 Processing helix chain 'A' and resid 184 through 217 Processing helix chain 'B' and resid 10 through 15 removed outlier: 3.961A pdb=" N LYS B 15 " --> pdb=" O GLY B 11 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 39 removed outlier: 4.336A pdb=" N LEU B 25 " --> pdb=" O GLY B 21 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N THR B 26 " --> pdb=" O LYS B 22 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ALA B 39 " --> pdb=" O ILE B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 47 removed outlier: 4.209A pdb=" N TRP B 44 " --> pdb=" O LYS B 41 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLY B 45 " --> pdb=" O GLU B 42 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N ASP B 46 " --> pdb=" O VAL B 43 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLU B 47 " --> pdb=" O TRP B 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 59 through 69 Processing helix chain 'B' and resid 72 through 101 Proline residue: B 87 - end of helix removed outlier: 3.520A pdb=" N ALA B 92 " --> pdb=" O ALA B 88 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N MET B 93 " --> pdb=" O LEU B 89 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ALA B 96 " --> pdb=" O ALA B 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 138 Processing helix chain 'B' and resid 138 through 159 removed outlier: 3.582A pdb=" N ILE B 145 " --> pdb=" O PHE B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 184 through 215 Processing sheet with id=AA1, first strand: chain 'A' and resid 52 through 53 Processing sheet with id=AA2, first strand: chain 'B' and resid 52 through 53 206 hydrogen bonds defined for protein. 600 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: 0.41 Time building geometry restraints manager: 0.37 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: 872 1.34 - 1.46: 847 1.46 - 1.58: 1378 1.58 - 1.69: 0 1.69 - 1.81: 42 Bond restraints: 3139 Sorted by residual: bond pdb=" C1 LMT A 304 " pdb=" C2 LMT A 304 " ideal model delta sigma weight residual 1.516 1.565 -0.049 2.00e-02 2.50e+03 6.04e+00 bond pdb=" C1 LMT B 302 " pdb=" C2 LMT B 302 " ideal model delta sigma weight residual 1.516 1.565 -0.049 2.00e-02 2.50e+03 5.98e+00 bond pdb=" C7 LMT B 301 " pdb=" C8 LMT B 301 " ideal model delta sigma weight residual 1.529 1.567 -0.038 2.00e-02 2.50e+03 3.64e+00 bond pdb=" C7 LMT A 305 " pdb=" C8 LMT A 305 " ideal model delta sigma weight residual 1.529 1.567 -0.038 2.00e-02 2.50e+03 3.63e+00 bond pdb=" C7 LMT B 304 " pdb=" C8 LMT B 304 " ideal model delta sigma weight residual 1.529 1.567 -0.038 2.00e-02 2.50e+03 3.61e+00 ... (remaining 3134 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.60: 4085 1.60 - 3.20: 85 3.20 - 4.80: 28 4.80 - 6.39: 26 6.39 - 7.99: 15 Bond angle restraints: 4239 Sorted by residual: angle pdb=" C6 LMT B 302 " pdb=" C7 LMT B 302 " pdb=" C8 LMT B 302 " ideal model delta sigma weight residual 117.26 109.27 7.99 3.00e+00 1.11e-01 7.10e+00 angle pdb=" C6 LMT B 301 " pdb=" C7 LMT B 301 " pdb=" C8 LMT B 301 " ideal model delta sigma weight residual 117.26 109.49 7.77 3.00e+00 1.11e-01 6.71e+00 angle pdb=" C6 LMT A 301 " pdb=" C7 LMT A 301 " pdb=" C8 LMT A 301 " ideal model delta sigma weight residual 117.26 109.56 7.70 3.00e+00 1.11e-01 6.59e+00 angle pdb=" C6 LMT B 304 " pdb=" C7 LMT B 304 " pdb=" C8 LMT B 304 " ideal model delta sigma weight residual 117.26 109.68 7.58 3.00e+00 1.11e-01 6.39e+00 angle pdb=" C2 LMT B 304 " pdb=" C3 LMT B 304 " pdb=" C4 LMT B 304 " ideal model delta sigma weight residual 117.09 109.52 7.57 3.00e+00 1.11e-01 6.37e+00 ... (remaining 4234 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.82: 1486 11.82 - 23.63: 223 23.63 - 35.45: 68 35.45 - 47.26: 26 47.26 - 59.08: 12 Dihedral angle restraints: 1815 sinusoidal: 735 harmonic: 1080 Sorted by residual: dihedral pdb=" CA PRO B 175 " pdb=" C PRO B 175 " pdb=" N ASN B 176 " pdb=" CA ASN B 176 " ideal model delta harmonic sigma weight residual -180.00 -159.26 -20.74 0 5.00e+00 4.00e-02 1.72e+01 dihedral pdb=" CA PRO A 175 " pdb=" C PRO A 175 " pdb=" N ASN A 176 " pdb=" CA ASN A 176 " ideal model delta harmonic sigma weight residual -180.00 -160.19 -19.81 0 5.00e+00 4.00e-02 1.57e+01 dihedral pdb=" CA GLU A 42 " pdb=" C GLU A 42 " pdb=" N VAL A 43 " pdb=" CA VAL A 43 " ideal model delta harmonic sigma weight residual 180.00 162.24 17.76 0 5.00e+00 4.00e-02 1.26e+01 ... (remaining 1812 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 291 0.032 - 0.064: 135 0.064 - 0.095: 39 0.095 - 0.127: 12 0.127 - 0.159: 2 Chirality restraints: 479 Sorted by residual: chirality pdb=" CA THR B 86 " pdb=" N THR B 86 " pdb=" C THR B 86 " pdb=" CB THR B 86 " both_signs ideal model delta sigma weight residual False 2.53 2.37 0.16 2.00e-01 2.50e+01 6.31e-01 chirality pdb=" CA THR A 86 " pdb=" N THR A 86 " pdb=" C THR A 86 " pdb=" CB THR A 86 " both_signs ideal model delta sigma weight residual False 2.53 2.37 0.16 2.00e-01 2.50e+01 6.11e-01 chirality pdb=" CA PRO B 185 " pdb=" N PRO B 185 " pdb=" C PRO B 185 " pdb=" CB PRO B 185 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.11 2.00e-01 2.50e+01 3.27e-01 ... (remaining 476 not shown) Planarity restraints: 500 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS A 174 " 0.024 5.00e-02 4.00e+02 3.61e-02 2.08e+00 pdb=" N PRO A 175 " -0.062 5.00e-02 4.00e+02 pdb=" CA PRO A 175 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 175 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 86 " 0.020 5.00e-02 4.00e+02 3.02e-02 1.46e+00 pdb=" N PRO B 87 " -0.052 5.00e-02 4.00e+02 pdb=" CA PRO B 87 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO B 87 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN A 57 " 0.012 5.00e-02 4.00e+02 1.83e-02 5.33e-01 pdb=" N PRO A 58 " -0.032 5.00e-02 4.00e+02 pdb=" CA PRO A 58 " 0.009 5.00e-02 4.00e+02 pdb=" CD PRO A 58 " 0.010 5.00e-02 4.00e+02 ... (remaining 497 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 29 2.68 - 3.23: 2894 3.23 - 3.79: 4300 3.79 - 4.34: 5872 4.34 - 4.90: 9832 Nonbonded interactions: 22927 Sorted by model distance: nonbonded pdb=" O ILE B 71 " pdb=" OH TYR B 158 " model vdw 2.122 3.040 nonbonded pdb=" O ILE A 71 " pdb=" OH TYR A 158 " model vdw 2.154 3.040 nonbonded pdb=" OH TYR B 68 " pdb=" O LYS B 168 " model vdw 2.278 3.040 nonbonded pdb=" OH TYR A 68 " pdb=" O LYS A 168 " model vdw 2.296 3.040 nonbonded pdb=" OD1 ASP A 66 " pdb=" O HOH A 401 " model vdw 2.335 3.040 ... (remaining 22922 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 9 through 302 or (resid 304 and (name C2 or name C3 or nam \ e C4 or name C5 or name C6 or name C7 or name C8 )))) selection = (chain 'B' and (resid 9 through 97 or resid 131 through 217 or (resid 301 and (n \ ame C3 or name C4 or name C5 or name C6 or name C7 or name C8 )) or (resid 302 a \ nd (name C5 or name C6 or name C7 )) or resid 304)) } 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: 0.350 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: 0.040 Check model and map are aligned: 0.000 Set scattering table: 0.030 Process input model: 5.050 Find NCS groups from input model: 0.040 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:8.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 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 : 0.006 0.049 3145 Z= 0.264 Angle : 0.861 7.993 4251 Z= 0.375 Chirality : 0.041 0.159 479 Planarity : 0.003 0.036 500 Dihedral : 13.928 59.078 1097 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: -0.99 (0.41), residues: 358 helix: -0.23 (0.31), residues: 238 sheet: 0.44 (0.95), residues: 28 loop : -1.85 (0.62), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 75 TYR 0.009 0.001 TYR B 65 PHE 0.010 0.001 PHE A 181 TRP 0.011 0.001 TRP B 134 HIS 0.002 0.001 HIS A 73 Details of bonding type rmsd covalent geometry : bond 0.00586 ( 3139) covalent geometry : angle 0.86047 ( 4239) SS BOND : bond 0.00172 ( 6) SS BOND : angle 0.92524 ( 12) hydrogen bonds : bond 0.27712 ( 206) hydrogen bonds : angle 7.29412 ( 600) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 716 Ramachandran restraints generated. 358 Oldfield, 0 Emsley, 358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 716 Ramachandran restraints generated. 358 Oldfield, 0 Emsley, 358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 30 time to evaluate : 0.121 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 30 average time/residue: 0.6414 time to fit residues: 19.7576 Evaluate side-chains 24 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 24 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 31 optimal weight: 0.6980 chunk 25 optimal weight: 0.8980 chunk 19 optimal weight: 0.8980 chunk 30 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 = 0.3669 r_free = 0.3669 target = 0.088816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.060670 restraints weight = 7884.341| |-----------------------------------------------------------------------------| r_work (start): 0.3012 rms_B_bonded: 2.41 r_work: 0.2878 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2765 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.1624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3145 Z= 0.154 Angle : 0.609 6.506 4251 Z= 0.332 Chirality : 0.042 0.149 479 Planarity : 0.004 0.035 500 Dihedral : 9.793 58.799 443 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 0.61 % Allowed : 7.01 % Favored : 92.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 1.15 (0.44), residues: 358 helix: 1.71 (0.33), residues: 239 sheet: 1.41 (1.10), residues: 22 loop : -1.90 (0.60), residues: 97 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 75 TYR 0.010 0.002 TYR B 212 PHE 0.011 0.001 PHE A 31 TRP 0.009 0.001 TRP A 133 HIS 0.002 0.001 HIS A 67 Details of bonding type rmsd covalent geometry : bond 0.00310 ( 3139) covalent geometry : angle 0.60807 ( 4239) SS BOND : bond 0.00224 ( 6) SS BOND : angle 0.90860 ( 12) hydrogen bonds : bond 0.07467 ( 206) hydrogen bonds : angle 3.94088 ( 600) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 716 Ramachandran restraints generated. 358 Oldfield, 0 Emsley, 358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 716 Ramachandran restraints generated. 358 Oldfield, 0 Emsley, 358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 32 time to evaluate : 0.122 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 33 average time/residue: 0.5617 time to fit residues: 19.1561 Evaluate side-chains 27 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 27 time to evaluate : 0.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 8 optimal weight: 2.9990 chunk 5 optimal weight: 0.6980 chunk 25 optimal weight: 0.9980 chunk 14 optimal weight: 0.8980 chunk 3 optimal weight: 0.9980 chunk 13 optimal weight: 0.6980 chunk 26 optimal weight: 3.9990 chunk 1 optimal weight: 30.0000 chunk 35 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.3680 r_free = 0.3680 target = 0.089680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.061703 restraints weight = 7878.247| |-----------------------------------------------------------------------------| r_work (start): 0.3039 rms_B_bonded: 2.37 r_work: 0.2903 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2789 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.2167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3145 Z= 0.135 Angle : 0.560 6.385 4251 Z= 0.306 Chirality : 0.041 0.163 479 Planarity : 0.004 0.032 500 Dihedral : 8.821 58.458 443 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 1.22 % Allowed : 10.67 % Favored : 88.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 2.02 (0.45), residues: 358 helix: 2.56 (0.33), residues: 239 sheet: 1.44 (1.11), residues: 22 loop : -2.03 (0.58), residues: 97 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 75 TYR 0.016 0.001 TYR B 158 PHE 0.011 0.001 PHE B 161 TRP 0.014 0.001 TRP A 133 HIS 0.002 0.001 HIS A 16 Details of bonding type rmsd covalent geometry : bond 0.00285 ( 3139) covalent geometry : angle 0.55903 ( 4239) SS BOND : bond 0.00165 ( 6) SS BOND : angle 0.78328 ( 12) hydrogen bonds : bond 0.05660 ( 206) hydrogen bonds : angle 3.48528 ( 600) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 716 Ramachandran restraints generated. 358 Oldfield, 0 Emsley, 358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 716 Ramachandran restraints generated. 358 Oldfield, 0 Emsley, 358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 29 time to evaluate : 0.113 Fit side-chains REVERT: A 212 TYR cc_start: 0.6641 (OUTLIER) cc_final: 0.6011 (t80) REVERT: B 97 TYR cc_start: 0.5224 (t80) cc_final: 0.4904 (t80) REVERT: B 151 MET cc_start: 0.9064 (mtp) cc_final: 0.8786 (mtm) outliers start: 4 outliers final: 0 residues processed: 31 average time/residue: 0.6020 time to fit residues: 19.1967 Evaluate side-chains 27 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 26 time to evaluate : 0.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 27 optimal weight: 8.9990 chunk 6 optimal weight: 1.9990 chunk 2 optimal weight: 8.9990 chunk 20 optimal weight: 0.5980 chunk 21 optimal weight: 3.9990 chunk 7 optimal weight: 0.8980 chunk 18 optimal weight: 20.0000 chunk 15 optimal weight: 0.5980 chunk 19 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3699 r_free = 0.3699 target = 0.090908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.062697 restraints weight = 7720.699| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 2.36 r_work: 0.2924 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2811 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.2390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3145 Z= 0.121 Angle : 0.553 8.343 4251 Z= 0.295 Chirality : 0.040 0.170 479 Planarity : 0.004 0.032 500 Dihedral : 8.147 57.394 443 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 2.74 % Allowed : 10.37 % Favored : 86.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 2.33 (0.45), residues: 358 helix: 2.87 (0.32), residues: 239 sheet: 1.51 (1.11), residues: 22 loop : -2.13 (0.57), residues: 97 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 75 TYR 0.008 0.001 TYR B 212 PHE 0.010 0.001 PHE A 31 TRP 0.010 0.001 TRP A 133 HIS 0.004 0.001 HIS B 16 Details of bonding type rmsd covalent geometry : bond 0.00256 ( 3139) covalent geometry : angle 0.55294 ( 4239) SS BOND : bond 0.00150 ( 6) SS BOND : angle 0.70326 ( 12) hydrogen bonds : bond 0.04911 ( 206) hydrogen bonds : angle 3.39981 ( 600) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 716 Ramachandran restraints generated. 358 Oldfield, 0 Emsley, 358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 716 Ramachandran restraints generated. 358 Oldfield, 0 Emsley, 358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 25 time to evaluate : 0.113 Fit side-chains REVERT: A 136 TYR cc_start: 0.6813 (OUTLIER) cc_final: 0.6494 (m-80) REVERT: A 212 TYR cc_start: 0.6618 (OUTLIER) cc_final: 0.5991 (t80) REVERT: B 97 TYR cc_start: 0.5031 (OUTLIER) cc_final: 0.4769 (t80) outliers start: 9 outliers final: 1 residues processed: 31 average time/residue: 0.5892 time to fit residues: 18.7794 Evaluate side-chains 29 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 25 time to evaluate : 0.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 TYR Chi-restraints excluded: chain A residue 163 MET Chi-restraints excluded: chain A residue 212 TYR Chi-restraints excluded: chain B residue 97 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 1 optimal weight: 30.0000 chunk 8 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 chunk 5 optimal weight: 0.0770 chunk 27 optimal weight: 8.9990 chunk 22 optimal weight: 0.8980 chunk 4 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 30 optimal weight: 6.9990 chunk 33 optimal weight: 0.5980 chunk 32 optimal weight: 1.9990 overall best weight: 0.7138 ------------------------------------------------------------------------------- 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 = 0.3706 r_free = 0.3706 target = 0.091414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.063230 restraints weight = 7707.939| |-----------------------------------------------------------------------------| r_work (start): 0.3075 rms_B_bonded: 2.34 r_work: 0.2943 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2831 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.2582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3145 Z= 0.121 Angle : 0.542 6.370 4251 Z= 0.292 Chirality : 0.040 0.168 479 Planarity : 0.004 0.030 500 Dihedral : 7.591 56.074 443 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.44 % Allowed : 12.20 % Favored : 85.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 2.52 (0.45), residues: 358 helix: 3.05 (0.32), residues: 239 sheet: 1.44 (1.10), residues: 22 loop : -2.14 (0.57), residues: 97 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 75 TYR 0.008 0.001 TYR B 158 PHE 0.009 0.001 PHE A 31 TRP 0.009 0.001 TRP A 133 HIS 0.001 0.001 HIS A 73 Details of bonding type rmsd covalent geometry : bond 0.00261 ( 3139) covalent geometry : angle 0.54161 ( 4239) SS BOND : bond 0.00144 ( 6) SS BOND : angle 0.66827 ( 12) hydrogen bonds : bond 0.04613 ( 206) hydrogen bonds : angle 3.32834 ( 600) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 716 Ramachandran restraints generated. 358 Oldfield, 0 Emsley, 358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 716 Ramachandran restraints generated. 358 Oldfield, 0 Emsley, 358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 28 time to evaluate : 0.114 Fit side-chains REVERT: A 136 TYR cc_start: 0.6934 (OUTLIER) cc_final: 0.6580 (m-80) REVERT: A 212 TYR cc_start: 0.6491 (OUTLIER) cc_final: 0.5883 (t80) REVERT: B 97 TYR cc_start: 0.5170 (OUTLIER) cc_final: 0.4842 (t80) REVERT: B 101 GLU cc_start: 0.4860 (OUTLIER) cc_final: 0.4221 (pt0) outliers start: 8 outliers final: 0 residues processed: 33 average time/residue: 0.6274 time to fit residues: 21.2485 Evaluate side-chains 29 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 25 time to evaluate : 0.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 TYR Chi-restraints excluded: chain A residue 212 TYR Chi-restraints excluded: chain B residue 97 TYR Chi-restraints excluded: chain B residue 101 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 8 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 25 optimal weight: 0.7980 chunk 15 optimal weight: 0.5980 chunk 0 optimal weight: 30.0000 chunk 18 optimal weight: 0.0270 chunk 14 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 overall best weight: 0.8842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 16 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.090859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.062536 restraints weight = 7704.108| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 2.36 r_work: 0.2934 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2821 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.2616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3145 Z= 0.128 Angle : 0.579 10.037 4251 Z= 0.304 Chirality : 0.040 0.169 479 Planarity : 0.004 0.031 500 Dihedral : 7.331 55.721 443 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 1.83 % Allowed : 15.24 % Favored : 82.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 2.62 (0.45), residues: 358 helix: 3.14 (0.32), residues: 239 sheet: 1.44 (1.10), residues: 22 loop : -2.09 (0.58), residues: 97 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 75 TYR 0.008 0.001 TYR B 158 PHE 0.009 0.001 PHE A 31 TRP 0.008 0.001 TRP A 133 HIS 0.017 0.002 HIS B 16 Details of bonding type rmsd covalent geometry : bond 0.00284 ( 3139) covalent geometry : angle 0.57870 ( 4239) SS BOND : bond 0.00144 ( 6) SS BOND : angle 0.65627 ( 12) hydrogen bonds : bond 0.04622 ( 206) hydrogen bonds : angle 3.32815 ( 600) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 716 Ramachandran restraints generated. 358 Oldfield, 0 Emsley, 358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 716 Ramachandran restraints generated. 358 Oldfield, 0 Emsley, 358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 26 time to evaluate : 0.124 Fit side-chains REVERT: A 136 TYR cc_start: 0.7035 (OUTLIER) cc_final: 0.6716 (m-80) REVERT: A 212 TYR cc_start: 0.6364 (OUTLIER) cc_final: 0.5720 (t80) REVERT: B 97 TYR cc_start: 0.5356 (OUTLIER) cc_final: 0.5061 (t80) outliers start: 6 outliers final: 0 residues processed: 30 average time/residue: 0.6734 time to fit residues: 20.7583 Evaluate side-chains 28 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 25 time to evaluate : 0.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 TYR Chi-restraints excluded: chain A residue 212 TYR Chi-restraints excluded: chain B residue 97 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 5 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 34 optimal weight: 0.8980 chunk 31 optimal weight: 4.9990 chunk 23 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 6 optimal weight: 0.5980 chunk 10 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 0 optimal weight: 30.0000 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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 = 0.3676 r_free = 0.3676 target = 0.089891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.061477 restraints weight = 7951.532| |-----------------------------------------------------------------------------| r_work (start): 0.3038 rms_B_bonded: 2.40 r_work: 0.2910 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2795 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.2584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3145 Z= 0.147 Angle : 0.574 6.693 4251 Z= 0.308 Chirality : 0.041 0.170 479 Planarity : 0.004 0.032 500 Dihedral : 7.379 56.157 443 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 2.74 % Allowed : 14.94 % Favored : 82.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 2.64 (0.45), residues: 358 helix: 3.14 (0.32), residues: 239 sheet: 1.40 (1.10), residues: 22 loop : -2.03 (0.59), residues: 97 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 75 TYR 0.010 0.001 TYR B 65 PHE 0.009 0.001 PHE A 31 TRP 0.007 0.001 TRP A 133 HIS 0.004 0.001 HIS B 16 Details of bonding type rmsd covalent geometry : bond 0.00346 ( 3139) covalent geometry : angle 0.57313 ( 4239) SS BOND : bond 0.00160 ( 6) SS BOND : angle 0.72825 ( 12) hydrogen bonds : bond 0.04925 ( 206) hydrogen bonds : angle 3.40631 ( 600) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 716 Ramachandran restraints generated. 358 Oldfield, 0 Emsley, 358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 716 Ramachandran restraints generated. 358 Oldfield, 0 Emsley, 358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 26 time to evaluate : 0.115 Fit side-chains REVERT: A 136 TYR cc_start: 0.7058 (OUTLIER) cc_final: 0.6724 (m-80) REVERT: A 212 TYR cc_start: 0.6340 (OUTLIER) cc_final: 0.5797 (t80) REVERT: B 97 TYR cc_start: 0.5375 (OUTLIER) cc_final: 0.5121 (t80) REVERT: B 101 GLU cc_start: 0.4788 (OUTLIER) cc_final: 0.4205 (pt0) outliers start: 9 outliers final: 1 residues processed: 34 average time/residue: 0.5357 time to fit residues: 18.7940 Evaluate side-chains 30 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 25 time to evaluate : 0.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 136 TYR Chi-restraints excluded: chain A residue 212 TYR Chi-restraints excluded: chain B residue 97 TYR Chi-restraints excluded: chain B residue 101 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 6 optimal weight: 2.9990 chunk 18 optimal weight: 0.1980 chunk 9 optimal weight: 6.9990 chunk 33 optimal weight: 0.9980 chunk 0 optimal weight: 30.0000 chunk 31 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 28 optimal weight: 5.9990 chunk 15 optimal weight: 0.9990 chunk 11 optimal weight: 4.9990 chunk 25 optimal weight: 0.4980 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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 = 0.3680 r_free = 0.3680 target = 0.090243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.061860 restraints weight = 7962.243| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 2.42 r_work: 0.2913 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2799 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.2666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3145 Z= 0.141 Angle : 0.615 11.068 4251 Z= 0.321 Chirality : 0.041 0.169 479 Planarity : 0.004 0.032 500 Dihedral : 7.331 56.100 443 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 1.52 % Allowed : 17.07 % Favored : 81.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 2.65 (0.45), residues: 358 helix: 3.10 (0.32), residues: 240 sheet: 1.38 (1.09), residues: 22 loop : -1.96 (0.60), residues: 96 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 75 TYR 0.008 0.001 TYR B 158 PHE 0.008 0.001 PHE A 31 TRP 0.007 0.001 TRP A 133 HIS 0.002 0.001 HIS B 16 Details of bonding type rmsd covalent geometry : bond 0.00328 ( 3139) covalent geometry : angle 0.61498 ( 4239) SS BOND : bond 0.00162 ( 6) SS BOND : angle 0.70809 ( 12) hydrogen bonds : bond 0.04840 ( 206) hydrogen bonds : angle 3.38597 ( 600) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 716 Ramachandran restraints generated. 358 Oldfield, 0 Emsley, 358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 716 Ramachandran restraints generated. 358 Oldfield, 0 Emsley, 358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 25 time to evaluate : 0.080 Fit side-chains REVERT: A 136 TYR cc_start: 0.7093 (OUTLIER) cc_final: 0.6785 (m-80) REVERT: A 212 TYR cc_start: 0.6333 (OUTLIER) cc_final: 0.5699 (t80) REVERT: B 97 TYR cc_start: 0.5373 (OUTLIER) cc_final: 0.5149 (t80) outliers start: 5 outliers final: 1 residues processed: 29 average time/residue: 0.5565 time to fit residues: 16.6550 Evaluate side-chains 29 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 25 time to evaluate : 0.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 136 TYR Chi-restraints excluded: chain A residue 212 TYR Chi-restraints excluded: chain B residue 97 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 1 optimal weight: 0.5980 chunk 8 optimal weight: 1.9990 chunk 7 optimal weight: 0.4980 chunk 23 optimal weight: 0.7980 chunk 15 optimal weight: 0.5980 chunk 25 optimal weight: 0.9980 chunk 18 optimal weight: 0.8980 chunk 33 optimal weight: 0.9980 chunk 4 optimal weight: 0.5980 chunk 34 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3704 r_free = 0.3704 target = 0.091599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.063460 restraints weight = 7956.673| |-----------------------------------------------------------------------------| r_work (start): 0.3077 rms_B_bonded: 2.41 r_work: 0.2952 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2837 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.2874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3145 Z= 0.117 Angle : 0.570 8.057 4251 Z= 0.305 Chirality : 0.040 0.167 479 Planarity : 0.004 0.031 500 Dihedral : 6.852 53.986 443 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 1.52 % Allowed : 17.07 % Favored : 81.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 2.74 (0.45), residues: 358 helix: 3.19 (0.31), residues: 240 sheet: 1.47 (1.11), residues: 22 loop : -1.99 (0.59), residues: 96 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 75 TYR 0.007 0.001 TYR A 97 PHE 0.008 0.001 PHE A 31 TRP 0.008 0.001 TRP A 133 HIS 0.002 0.000 HIS B 16 Details of bonding type rmsd covalent geometry : bond 0.00254 ( 3139) covalent geometry : angle 0.56977 ( 4239) SS BOND : bond 0.00124 ( 6) SS BOND : angle 0.63807 ( 12) hydrogen bonds : bond 0.04194 ( 206) hydrogen bonds : angle 3.29292 ( 600) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 716 Ramachandran restraints generated. 358 Oldfield, 0 Emsley, 358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 716 Ramachandran restraints generated. 358 Oldfield, 0 Emsley, 358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 29 time to evaluate : 0.127 Fit side-chains REVERT: A 136 TYR cc_start: 0.7025 (OUTLIER) cc_final: 0.6734 (m-80) REVERT: A 212 TYR cc_start: 0.6240 (OUTLIER) cc_final: 0.5667 (t80) REVERT: B 136 TYR cc_start: 0.7629 (t80) cc_final: 0.7316 (t80) REVERT: B 212 TYR cc_start: 0.6369 (t80) cc_final: 0.6009 (t80) outliers start: 5 outliers final: 1 residues processed: 33 average time/residue: 0.5975 time to fit residues: 20.3060 Evaluate side-chains 29 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 26 time to evaluate : 0.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 136 TYR Chi-restraints excluded: chain A residue 212 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 18 optimal weight: 0.5980 chunk 17 optimal weight: 4.9990 chunk 26 optimal weight: 10.0000 chunk 9 optimal weight: 5.9990 chunk 16 optimal weight: 0.9980 chunk 27 optimal weight: 6.9990 chunk 33 optimal weight: 2.9990 chunk 34 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 chunk 1 optimal weight: 20.0000 chunk 22 optimal weight: 0.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 206 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.090772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.062534 restraints weight = 7896.071| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 2.43 r_work: 0.2933 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2820 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.2835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3145 Z= 0.140 Angle : 0.625 10.722 4251 Z= 0.325 Chirality : 0.041 0.169 479 Planarity : 0.004 0.032 500 Dihedral : 6.886 53.900 443 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 0.91 % Allowed : 17.68 % Favored : 81.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 2.67 (0.45), residues: 358 helix: 3.15 (0.32), residues: 241 sheet: 1.39 (1.09), residues: 22 loop : -2.09 (0.58), residues: 95 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 75 TYR 0.024 0.002 TYR B 97 PHE 0.008 0.001 PHE A 31 TRP 0.007 0.001 TRP A 133 HIS 0.002 0.000 HIS A 16 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 3139) covalent geometry : angle 0.62454 ( 4239) SS BOND : bond 0.00148 ( 6) SS BOND : angle 0.67147 ( 12) hydrogen bonds : bond 0.04552 ( 206) hydrogen bonds : angle 3.41237 ( 600) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 716 Ramachandran restraints generated. 358 Oldfield, 0 Emsley, 358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 716 Ramachandran restraints generated. 358 Oldfield, 0 Emsley, 358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 26 time to evaluate : 0.119 Fit side-chains REVERT: A 136 TYR cc_start: 0.7076 (OUTLIER) cc_final: 0.6795 (m-80) REVERT: A 212 TYR cc_start: 0.6260 (OUTLIER) cc_final: 0.5673 (t80) REVERT: B 212 TYR cc_start: 0.6380 (t80) cc_final: 0.6014 (t80) outliers start: 3 outliers final: 1 residues processed: 29 average time/residue: 0.6111 time to fit residues: 18.2350 Evaluate side-chains 28 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 25 time to evaluate : 0.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 136 TYR Chi-restraints excluded: chain A residue 212 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 33 optimal weight: 0.8980 chunk 23 optimal weight: 0.6980 chunk 19 optimal weight: 3.9990 chunk 11 optimal weight: 0.8980 chunk 34 optimal weight: 0.9980 chunk 6 optimal weight: 2.9990 chunk 35 optimal weight: 4.9990 chunk 7 optimal weight: 1.9990 chunk 27 optimal weight: 9.9990 chunk 20 optimal weight: 0.9990 chunk 17 optimal weight: 7.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 = 0.3695 r_free = 0.3695 target = 0.090907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.062647 restraints weight = 7993.771| |-----------------------------------------------------------------------------| r_work (start): 0.3065 rms_B_bonded: 2.42 r_work: 0.2939 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2825 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.2851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 3145 Z= 0.131 Angle : 0.601 8.341 4251 Z= 0.321 Chirality : 0.040 0.168 479 Planarity : 0.004 0.031 500 Dihedral : 6.843 53.249 443 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 0.91 % Allowed : 18.29 % Favored : 80.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 2.67 (0.45), residues: 358 helix: 3.14 (0.32), residues: 241 sheet: 1.43 (1.10), residues: 22 loop : -2.09 (0.59), residues: 95 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 75 TYR 0.025 0.002 TYR B 97 PHE 0.008 0.001 PHE A 31 TRP 0.007 0.001 TRP A 133 HIS 0.002 0.000 HIS B 16 Details of bonding type rmsd covalent geometry : bond 0.00300 ( 3139) covalent geometry : angle 0.60116 ( 4239) SS BOND : bond 0.00144 ( 6) SS BOND : angle 0.65242 ( 12) hydrogen bonds : bond 0.04446 ( 206) hydrogen bonds : angle 3.37705 ( 600) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1444.05 seconds wall clock time: 25 minutes 14.59 seconds (1514.59 seconds total)