Starting phenix.real_space_refine on Tue Aug 4 17:50:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ygi_72925/08_2026/9ygi_72925.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ygi_72925/08_2026/9ygi_72925.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ygi_72925/08_2026/9ygi_72925.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ygi_72925/08_2026/9ygi_72925.map" model { file = "/net/cci-nas-00/data/ceres_data/9ygi_72925/08_2026/9ygi_72925.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ygi_72925/08_2026/9ygi_72925.cif" } resolution = 3.98 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= 0.018 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 21 5.16 5 C 3505 2.51 5 N 948 2.21 5 O 1050 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 5524 Number of models: 1 Model: "" Number of chains: 7 Chain: "H" Number of atoms: 943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 943 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "L" Number of atoms: 836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 836 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "M" Number of atoms: 943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 943 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "N" Number of atoms: 836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 836 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "O" Number of atoms: 943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 943 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "P" Number of atoms: 836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 836 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "G" Number of atoms: 187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 187 Classifications: {'peptide': 26} Link IDs: {'PTRANS': 6, 'TRANS': 19} Time building chain proxies: 1.37, per 1000 atoms: 0.25 Number of scatterers: 5524 At special positions: 0 Unit cell: (85.49, 98.77, 98.77, 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 21 16.00 O 1050 8.00 N 948 7.00 C 3505 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 92 " distance=2.04 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.03 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 92 " distance=2.04 Simple disulfide: pdb=" SG CYS P 23 " - pdb=" SG CYS P 88 " distance=2.04 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: 0.40 Conformation dependent library (CDL) restraints added in 188.8 milliseconds 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1276 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 17 sheets defined 5.7% alpha, 37.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.11 Creating SS restraints... Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.722A pdb=" N THR H 87 " --> pdb=" O ALA H 84 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.623A pdb=" N VAL L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'M' and resid 61 through 64 removed outlier: 4.083A pdb=" N LYS M 64 " --> pdb=" O ASP M 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 61 through 64' Processing helix chain 'M' and resid 83 through 87 removed outlier: 3.589A pdb=" N THR M 87 " --> pdb=" O ALA M 84 " (cutoff:3.500A) Processing helix chain 'O' and resid 53 through 55 No H-bonds generated for 'chain 'O' and resid 53 through 55' Processing helix chain 'O' and resid 61 through 64 removed outlier: 3.921A pdb=" N LYS O 64 " --> pdb=" O ASP O 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 61 through 64' Processing helix chain 'O' and resid 83 through 87 removed outlier: 3.629A pdb=" N THR O 87 " --> pdb=" O ALA O 84 " (cutoff:3.500A) Processing helix chain 'P' and resid 79 through 83 removed outlier: 3.918A pdb=" N VAL P 83 " --> pdb=" O PRO P 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 4 through 7 Processing sheet with id=AA2, first strand: chain 'H' and resid 10 through 11 removed outlier: 3.511A pdb=" N GLY H 10 " --> pdb=" O LEU H 108 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N THR H 110 " --> pdb=" O GLY H 10 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N TYR H 58 " --> pdb=" O VAL H 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 96 through 97 removed outlier: 3.895A pdb=" N PHE H 96 " --> pdb=" O PHE H 100C" (cutoff:3.500A) removed outlier: 3.550A pdb=" N PHE H 100C" --> pdb=" O PHE H 96 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'L' and resid 4 through 6 Processing sheet with id=AA5, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.676A pdb=" N ALA L 13 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'M' and resid 5 through 7 Processing sheet with id=AA7, first strand: chain 'M' and resid 10 through 11 removed outlier: 3.958A pdb=" N GLY M 10 " --> pdb=" O LEU M 108 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N THR M 110 " --> pdb=" O GLY M 10 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N MET M 34 " --> pdb=" O VAL M 50 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N VAL M 50 " --> pdb=" O MET M 34 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N TRP M 36 " --> pdb=" O VAL M 48 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'M' and resid 96 through 97 removed outlier: 3.818A pdb=" N PHE M 96 " --> pdb=" O PHE M 100C" (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 4 through 5 Processing sheet with id=AB1, first strand: chain 'N' and resid 10 through 13 removed outlier: 6.378A pdb=" N TRP N 35 " --> pdb=" O LEU N 47 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'N' and resid 10 through 13 removed outlier: 4.094A pdb=" N GLU N 90 " --> pdb=" O THR N 97 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N THR N 97 " --> pdb=" O GLU N 90 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'O' and resid 3 through 7 Processing sheet with id=AB4, first strand: chain 'O' and resid 10 through 12 removed outlier: 6.429A pdb=" N GLY O 10 " --> pdb=" O THR O 110 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N ARG O 38 " --> pdb=" O TRP O 47 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N TRP O 47 " --> pdb=" O ARG O 38 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N TYR O 58 " --> pdb=" O VAL O 50 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'O' and resid 96 through 98 Processing sheet with id=AB6, first strand: chain 'P' and resid 4 through 6 Processing sheet with id=AB7, first strand: chain 'P' and resid 10 through 13 removed outlier: 3.558A pdb=" N ALA P 13 " --> pdb=" O GLU P 105 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N TRP P 35 " --> pdb=" O LEU P 47 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'P' and resid 10 through 13 removed outlier: 3.558A pdb=" N ALA P 13 " --> pdb=" O GLU P 105 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLU P 90 " --> pdb=" O THR P 97 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N THR P 97 " --> pdb=" O GLU P 90 " (cutoff:3.500A) 190 hydrogen bonds defined for protein. 456 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: 0.70 Time building geometry restraints manager: 0.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1769 1.34 - 1.46: 1454 1.46 - 1.58: 2414 1.58 - 1.70: 0 1.70 - 1.82: 30 Bond restraints: 5667 Sorted by residual: bond pdb=" N ASN G 121 " pdb=" CA ASN G 121 " ideal model delta sigma weight residual 1.456 1.487 -0.031 1.22e-02 6.72e+03 6.42e+00 bond pdb=" N ASP G 119 " pdb=" CA ASP G 119 " ideal model delta sigma weight residual 1.458 1.485 -0.027 1.25e-02 6.40e+03 4.64e+00 bond pdb=" N GLN H 1 " pdb=" CA GLN H 1 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.90e-02 2.77e+03 3.20e+00 bond pdb=" N ASN G 105 " pdb=" CA ASN G 105 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.06e+00 bond pdb=" N ASP P 1 " pdb=" CA ASP P 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.02e+00 ... (remaining 5662 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.00: 7109 1.00 - 2.00: 453 2.00 - 3.00: 85 3.00 - 4.01: 37 4.01 - 5.01: 8 Bond angle restraints: 7692 Sorted by residual: angle pdb=" N SER O 82B" pdb=" CA SER O 82B" pdb=" CB SER O 82B" ideal model delta sigma weight residual 114.17 109.82 4.35 1.14e+00 7.69e-01 1.46e+01 angle pdb=" CA ASN G 121 " pdb=" C ASN G 121 " pdb=" O ASN G 121 " ideal model delta sigma weight residual 120.81 117.59 3.22 1.15e+00 7.56e-01 7.82e+00 angle pdb=" C THR M 30 " pdb=" N THR M 31 " pdb=" CA THR M 31 " ideal model delta sigma weight residual 121.54 126.38 -4.84 1.91e+00 2.74e-01 6.43e+00 angle pdb=" CA GLY M 106 " pdb=" C GLY M 106 " pdb=" O GLY M 106 " ideal model delta sigma weight residual 122.39 120.19 2.20 9.30e-01 1.16e+00 5.60e+00 angle pdb=" CA GLY P 66 " pdb=" C GLY P 66 " pdb=" O GLY P 66 " ideal model delta sigma weight residual 122.24 120.19 2.05 8.70e-01 1.32e+00 5.57e+00 ... (remaining 7687 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.82: 2802 17.82 - 35.64: 373 35.64 - 53.45: 110 53.45 - 71.27: 13 71.27 - 89.09: 3 Dihedral angle restraints: 3301 sinusoidal: 1289 harmonic: 2012 Sorted by residual: dihedral pdb=" CB CYS M 22 " pdb=" SG CYS M 22 " pdb=" SG CYS M 92 " pdb=" CB CYS M 92 " ideal model delta sinusoidal sigma weight residual 93.00 31.76 61.24 1 1.00e+01 1.00e-02 4.98e+01 dihedral pdb=" CA THR P 69 " pdb=" C THR P 69 " pdb=" N HIS P 70 " pdb=" CA HIS P 70 " ideal model delta harmonic sigma weight residual -180.00 -158.13 -21.87 0 5.00e+00 4.00e-02 1.91e+01 dihedral pdb=" CB CYS O 22 " pdb=" SG CYS O 22 " pdb=" SG CYS O 92 " pdb=" CB CYS O 92 " ideal model delta sinusoidal sigma weight residual 93.00 56.48 36.52 1 1.00e+01 1.00e-02 1.88e+01 ... (remaining 3298 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 574 0.039 - 0.078: 163 0.078 - 0.117: 70 0.117 - 0.156: 12 0.156 - 0.195: 2 Chirality restraints: 821 Sorted by residual: chirality pdb=" CB THR M 31 " pdb=" CA THR M 31 " pdb=" OG1 THR M 31 " pdb=" CG2 THR M 31 " both_signs ideal model delta sigma weight residual False 2.55 2.36 0.19 2.00e-01 2.50e+01 9.49e-01 chirality pdb=" CA ILE M 57 " pdb=" N ILE M 57 " pdb=" C ILE M 57 " pdb=" CB ILE M 57 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.44e-01 chirality pdb=" CA ILE M 51 " pdb=" N ILE M 51 " pdb=" C ILE M 51 " pdb=" CB ILE M 51 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.51e-01 ... (remaining 818 not shown) Planarity restraints: 986 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL N 58 " -0.023 5.00e-02 4.00e+02 3.47e-02 1.93e+00 pdb=" N PRO N 59 " 0.060 5.00e-02 4.00e+02 pdb=" CA PRO N 59 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO N 59 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR M 30 " 0.007 2.00e-02 2.50e+03 1.33e-02 1.77e+00 pdb=" C THR M 30 " -0.023 2.00e-02 2.50e+03 pdb=" O THR M 30 " 0.009 2.00e-02 2.50e+03 pdb=" N THR M 31 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN G 129 " 0.006 2.00e-02 2.50e+03 1.28e-02 1.63e+00 pdb=" C ASN G 129 " -0.022 2.00e-02 2.50e+03 pdb=" O ASN G 129 " 0.008 2.00e-02 2.50e+03 pdb=" N ALA G 130 " 0.007 2.00e-02 2.50e+03 ... (remaining 983 not shown) Histogram of nonbonded interaction distances: 1.86 - 2.47: 58 2.47 - 3.08: 3705 3.08 - 3.69: 7958 3.69 - 4.29: 11031 4.29 - 4.90: 19084 Nonbonded interactions: 41836 Sorted by model distance: nonbonded pdb=" OG1 THR O 68 " pdb=" OE1 GLN O 81 " model vdw 1.863 3.040 nonbonded pdb=" OD1 ASP O 86 " pdb=" OH TYR O 90 " model vdw 1.965 3.040 nonbonded pdb=" OG SER P 63 " pdb=" OG1 THR P 74 " model vdw 2.009 3.040 nonbonded pdb=" OD1 ASP P 82 " pdb=" OH TYR P 86 " model vdw 2.033 3.040 nonbonded pdb=" OE1 GLU O 23 " pdb=" OG1 THR O 77 " model vdw 2.035 3.040 ... (remaining 41831 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 'H' selection = chain 'M' selection = chain 'O' } ncs_group { reference = chain 'L' selection = chain 'N' selection = chain 'P' } 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 group one per residue 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: 4.330 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: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 5.900 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.000 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: 0.010 Load rotamer database and sin/cos tables:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 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 : 0.003 0.034 5673 Z= 0.146 Angle : 0.598 5.007 7704 Z= 0.335 Chirality : 0.045 0.195 821 Planarity : 0.003 0.035 986 Dihedral : 16.771 89.088 2007 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.58 % Allowed : 8.70 % Favored : 90.72 % Rotamer: Outliers : 0.00 % Allowed : 33.11 % Favored : 66.89 % 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: -0.41 (0.33), residues: 690 helix: None (None), residues: 0 sheet: 0.89 (0.33), residues: 267 loop : -1.11 (0.31), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG N 96 TYR 0.010 0.001 TYR P 49 PHE 0.014 0.001 PHE H 96 TRP 0.014 0.001 TRP L 32 HIS 0.004 0.001 HIS M 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.15 ( 5667) covalent geometry : angle 0.59605 / 0.33 ( 7692) SS BOND : bond 0.00568 / 0.35 ( 6) SS BOND : angle 1.43157 / 1.08 ( 12) hydrogen bonds : bond 0.11380 / 8.64 ( 181) hydrogen bonds : angle 7.09728 / 4.72 ( 456) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 162 time to evaluate : 0.196 Fit side-chains revert: symmetry clash REVERT: H 36 TRP cc_start: 0.8806 (m100) cc_final: 0.8283 (m100) REVERT: H 43 LYS cc_start: 0.8220 (mttp) cc_final: 0.7685 (mptt) REVERT: L 1 ASP cc_start: 0.8330 (m-30) cc_final: 0.7207 (p0) REVERT: L 32 TRP cc_start: 0.8196 (m-10) cc_final: 0.7834 (m-10) REVERT: M 47 TRP cc_start: 0.9023 (t60) cc_final: 0.8804 (t60) REVERT: M 85 GLU cc_start: 0.7692 (pm20) cc_final: 0.7468 (pm20) REVERT: N 31 ARG cc_start: 0.8000 (mmm-85) cc_final: 0.7055 (tpt170) REVERT: N 56 ASN cc_start: 0.7911 (p0) cc_final: 0.7707 (p0) REVERT: O 5 VAL cc_start: 0.7538 (m) cc_final: 0.7317 (t) REVERT: O 47 TRP cc_start: 0.8693 (t60) cc_final: 0.8447 (t60) REVERT: P 36 TYR cc_start: 0.7992 (m-80) cc_final: 0.7597 (m-80) REVERT: P 90 GLU cc_start: 0.8697 (pp20) cc_final: 0.8109 (pm20) outliers start: 0 outliers final: 0 residues processed: 162 average time/residue: 0.0675 time to fit residues: 14.5641 Evaluate side-chains 132 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 132 time to evaluate : 0.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 49 optimal weight: 5.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.0050 chunk 33 optimal weight: 8.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 6.9990 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 0.7980 chunk 27 optimal weight: 0.0030 chunk 64 optimal weight: 0.7980 overall best weight: 0.5204 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... N 38 GLN N 79 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.176660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.145573 restraints weight = 8931.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.148864 restraints weight = 6517.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.151041 restraints weight = 5268.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.152256 restraints weight = 4550.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.153311 restraints weight = 4143.699| |-----------------------------------------------------------------------------| r_work (final): 0.3801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 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 0.030 5673 Z= 0.143 Angle : 0.645 9.900 7704 Z= 0.340 Chirality : 0.045 0.152 821 Planarity : 0.004 0.041 986 Dihedral : 4.529 18.659 772 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.58 % Allowed : 6.81 % Favored : 92.61 % Rotamer: Outliers : 5.38 % Allowed : 30.59 % Favored : 64.03 % 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: -0.27 (0.33), residues: 690 helix: None (None), residues: 0 sheet: 1.11 (0.33), residues: 264 loop : -1.09 (0.31), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG M 71 TYR 0.013 0.002 TYR N 49 PHE 0.028 0.002 PHE L 71 TRP 0.009 0.001 TRP O 36 HIS 0.008 0.002 HIS O 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.14 ( 5667) covalent geometry : angle 0.64337 / 0.34 ( 7692) SS BOND : bond 0.00564 / 0.35 ( 6) SS BOND : angle 1.18411 / 0.78 ( 12) hydrogen bonds : bond 0.03757 / 2.47 ( 181) hydrogen bonds : angle 5.58001 / 3.82 ( 456) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 136 time to evaluate : 0.127 Fit side-chains revert: symmetry clash REVERT: L 1 ASP cc_start: 0.8035 (m-30) cc_final: 0.7309 (p0) REVERT: L 32 TRP cc_start: 0.8297 (m-10) cc_final: 0.8078 (m-10) REVERT: M 47 TRP cc_start: 0.9050 (t60) cc_final: 0.8757 (t60) REVERT: M 61 ASP cc_start: 0.5163 (p0) cc_final: 0.4907 (p0) REVERT: M 82 MET cc_start: 0.3895 (mmp) cc_final: 0.3488 (mmp) REVERT: M 85 GLU cc_start: 0.7727 (pm20) cc_final: 0.7429 (pm20) REVERT: M 87 THR cc_start: 0.8390 (p) cc_final: 0.8149 (p) REVERT: N 31 ARG cc_start: 0.7709 (mmm-85) cc_final: 0.6890 (tpt170) REVERT: O 23 GLU cc_start: 0.7098 (pp20) cc_final: 0.6521 (mt-10) REVERT: O 47 TRP cc_start: 0.8747 (t60) cc_final: 0.8537 (t60) REVERT: O 82 MET cc_start: 0.5521 (mmp) cc_final: 0.5224 (mmp) REVERT: P 36 TYR cc_start: 0.8486 (m-80) cc_final: 0.8192 (m-10) outliers start: 32 outliers final: 18 residues processed: 152 average time/residue: 0.0612 time to fit residues: 12.1916 Evaluate side-chains 142 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 124 time to evaluate : 0.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain L residue 49 TYR Chi-restraints excluded: chain M residue 18 LEU Chi-restraints excluded: chain M residue 62 SER Chi-restraints excluded: chain M residue 107 THR Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 19 VAL Chi-restraints excluded: chain N residue 38 GLN Chi-restraints excluded: chain N residue 49 TYR Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain O residue 62 SER Chi-restraints excluded: chain P residue 26 SER Chi-restraints excluded: chain P residue 37 GLN Chi-restraints excluded: chain P residue 68 GLU Chi-restraints excluded: chain P residue 100 GLN Chi-restraints excluded: chain G residue 118 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 20 optimal weight: 0.5980 chunk 57 optimal weight: 0.7980 chunk 1 optimal weight: 0.0170 chunk 0 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 6 optimal weight: 0.0030 chunk 11 optimal weight: 0.0370 chunk 47 optimal weight: 3.9990 chunk 28 optimal weight: 0.4980 chunk 63 optimal weight: 0.0050 chunk 32 optimal weight: 0.6980 overall best weight: 0.1120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... M 35 HIS P 70 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.180388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.150599 restraints weight = 8872.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.153664 restraints weight = 6528.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.155633 restraints weight = 5304.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.157268 restraints weight = 4581.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.158091 restraints weight = 4121.471| |-----------------------------------------------------------------------------| r_work (final): 0.3873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.2335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5673 Z= 0.116 Angle : 0.630 10.260 7704 Z= 0.329 Chirality : 0.045 0.158 821 Planarity : 0.004 0.045 986 Dihedral : 4.331 17.373 772 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.58 % Allowed : 5.51 % Favored : 93.91 % Rotamer: Outliers : 4.03 % Allowed : 29.41 % Favored : 66.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.34), residues: 690 helix: None (None), residues: 0 sheet: 1.14 (0.33), residues: 263 loop : -0.97 (0.31), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG O 19 TYR 0.014 0.001 TYR L 91 PHE 0.019 0.001 PHE L 71 TRP 0.017 0.001 TRP N 35 HIS 0.005 0.001 HIS M 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.12 ( 5667) covalent geometry : angle 0.62909 / 0.33 ( 7692) SS BOND : bond 0.00698 / 0.39 ( 6) SS BOND : angle 1.19005 / 0.84 ( 12) hydrogen bonds : bond 0.03202 / 2.08 ( 181) hydrogen bonds : angle 5.24234 / 3.60 ( 456) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 130 time to evaluate : 0.170 Fit side-chains revert: symmetry clash REVERT: H 34 MET cc_start: 0.7642 (ttt) cc_final: 0.7290 (ttt) REVERT: L 1 ASP cc_start: 0.7960 (m-30) cc_final: 0.7299 (p0) REVERT: M 47 TRP cc_start: 0.8861 (t60) cc_final: 0.8614 (t60) REVERT: M 85 GLU cc_start: 0.7696 (pm20) cc_final: 0.7375 (pm20) REVERT: M 87 THR cc_start: 0.8299 (p) cc_final: 0.8093 (p) REVERT: N 31 ARG cc_start: 0.7728 (mmm-85) cc_final: 0.7025 (tpt170) REVERT: O 23 GLU cc_start: 0.7141 (pp20) cc_final: 0.6360 (mt-10) REVERT: P 36 TYR cc_start: 0.8408 (m-80) cc_final: 0.8175 (m-10) outliers start: 24 outliers final: 14 residues processed: 147 average time/residue: 0.0587 time to fit residues: 11.4903 Evaluate side-chains 133 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 119 time to evaluate : 0.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain L residue 29 ILE Chi-restraints excluded: chain M residue 51 ILE Chi-restraints excluded: chain M residue 107 THR Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 19 VAL Chi-restraints excluded: chain N residue 49 TYR Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain O residue 62 SER Chi-restraints excluded: chain O residue 87 THR Chi-restraints excluded: chain P residue 68 GLU Chi-restraints excluded: chain P residue 100 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 15 optimal weight: 0.0980 chunk 64 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 14 optimal weight: 0.6980 chunk 57 optimal weight: 0.1980 chunk 26 optimal weight: 0.2980 chunk 22 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 0 optimal weight: 0.6980 chunk 38 optimal weight: 7.9990 overall best weight: 0.3980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... N 38 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.177268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.146659 restraints weight = 8933.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.149791 restraints weight = 6479.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.151985 restraints weight = 5244.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.153390 restraints weight = 4529.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.154249 restraints weight = 4086.700| |-----------------------------------------------------------------------------| r_work (final): 0.3840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.2634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5673 Z= 0.124 Angle : 0.625 11.520 7704 Z= 0.325 Chirality : 0.045 0.171 821 Planarity : 0.004 0.046 986 Dihedral : 4.355 17.619 772 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.58 % Allowed : 6.67 % Favored : 92.75 % Rotamer: Outliers : 4.03 % Allowed : 30.25 % Favored : 65.71 % 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: -0.15 (0.33), residues: 690 helix: None (None), residues: 0 sheet: 1.17 (0.33), residues: 259 loop : -0.97 (0.31), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG N 96 TYR 0.014 0.001 TYR P 91 PHE 0.027 0.002 PHE O 52A TRP 0.028 0.001 TRP L 32 HIS 0.004 0.001 HIS H 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.12 ( 5667) covalent geometry : angle 0.62241 / 0.32 ( 7692) SS BOND : bond 0.00584 / 0.38 ( 6) SS BOND : angle 1.43749 / 1.01 ( 12) hydrogen bonds : bond 0.03298 / 2.13 ( 181) hydrogen bonds : angle 5.16745 / 3.52 ( 456) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 129 time to evaluate : 0.232 Fit side-chains REVERT: L 32 TRP cc_start: 0.8235 (m-10) cc_final: 0.7917 (m-10) REVERT: M 47 TRP cc_start: 0.8876 (t60) cc_final: 0.8642 (t60) REVERT: M 85 GLU cc_start: 0.7711 (pm20) cc_final: 0.7306 (pm20) REVERT: N 31 ARG cc_start: 0.7666 (mmm-85) cc_final: 0.7042 (tpt170) REVERT: O 23 GLU cc_start: 0.7258 (pp20) cc_final: 0.6390 (mt-10) REVERT: P 36 TYR cc_start: 0.8524 (m-80) cc_final: 0.8313 (m-10) outliers start: 24 outliers final: 17 residues processed: 146 average time/residue: 0.0604 time to fit residues: 11.9043 Evaluate side-chains 133 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 116 time to evaluate : 0.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 29 ILE Chi-restraints excluded: chain M residue 51 ILE Chi-restraints excluded: chain M residue 62 SER Chi-restraints excluded: chain M residue 107 THR Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 10 THR Chi-restraints excluded: chain N residue 19 VAL Chi-restraints excluded: chain N residue 49 TYR Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain O residue 82 SER Chi-restraints excluded: chain O residue 87 THR Chi-restraints excluded: chain P residue 26 SER Chi-restraints excluded: chain P residue 68 GLU Chi-restraints excluded: chain P residue 100 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 18 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 47 optimal weight: 0.3980 chunk 23 optimal weight: 4.9990 chunk 29 optimal weight: 0.9990 chunk 52 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 24 optimal weight: 0.8980 chunk 12 optimal weight: 0.7980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... O 39 GLN P 38 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.171467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.140123 restraints weight = 9186.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.143113 restraints weight = 6712.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.145196 restraints weight = 5476.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.146341 restraints weight = 4782.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.147487 restraints weight = 4366.976| |-----------------------------------------------------------------------------| r_work (final): 0.3766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.2910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 5673 Z= 0.168 Angle : 0.654 11.627 7704 Z= 0.342 Chirality : 0.046 0.255 821 Planarity : 0.004 0.047 986 Dihedral : 4.666 18.344 772 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.58 % Allowed : 7.68 % Favored : 91.74 % Rotamer: Outliers : 4.87 % Allowed : 30.25 % Favored : 64.87 % 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: -0.33 (0.33), residues: 690 helix: None (None), residues: 0 sheet: 0.88 (0.33), residues: 267 loop : -1.00 (0.31), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG N 96 TYR 0.018 0.002 TYR N 49 PHE 0.035 0.002 PHE L 71 TRP 0.013 0.002 TRP L 32 HIS 0.007 0.001 HIS H 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.17 ( 5667) covalent geometry : angle 0.65191 / 0.34 ( 7692) SS BOND : bond 0.00516 / 0.35 ( 6) SS BOND : angle 1.53619 / 1.13 ( 12) hydrogen bonds : bond 0.03566 / 2.32 ( 181) hydrogen bonds : angle 5.33032 / 3.65 ( 456) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 123 time to evaluate : 0.213 Fit side-chains REVERT: H 76 ASN cc_start: 0.7493 (m110) cc_final: 0.7235 (m-40) REVERT: L 32 TRP cc_start: 0.8267 (OUTLIER) cc_final: 0.8013 (m-10) REVERT: M 47 TRP cc_start: 0.8981 (t60) cc_final: 0.8748 (t60) REVERT: M 85 GLU cc_start: 0.7684 (pm20) cc_final: 0.7229 (pm20) REVERT: N 31 ARG cc_start: 0.7768 (mmm-85) cc_final: 0.7016 (tpt170) REVERT: P 42 LYS cc_start: 0.8489 (mmmm) cc_final: 0.8253 (tttt) REVERT: P 48 ILE cc_start: 0.8322 (mm) cc_final: 0.8010 (mm) REVERT: G 107 ASN cc_start: 0.8190 (p0) cc_final: 0.7807 (p0) REVERT: G 117 ASN cc_start: 0.8173 (m-40) cc_final: 0.7822 (m-40) outliers start: 29 outliers final: 23 residues processed: 141 average time/residue: 0.0641 time to fit residues: 12.0950 Evaluate side-chains 140 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 116 time to evaluate : 0.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 29 ILE Chi-restraints excluded: chain L residue 32 TRP Chi-restraints excluded: chain L residue 49 TYR Chi-restraints excluded: chain M residue 18 LEU Chi-restraints excluded: chain M residue 51 ILE Chi-restraints excluded: chain M residue 62 SER Chi-restraints excluded: chain M residue 107 THR Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 10 THR Chi-restraints excluded: chain N residue 19 VAL Chi-restraints excluded: chain N residue 49 TYR Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain O residue 20 LEU Chi-restraints excluded: chain O residue 28 ILE Chi-restraints excluded: chain O residue 62 SER Chi-restraints excluded: chain O residue 87 THR Chi-restraints excluded: chain P residue 26 SER Chi-restraints excluded: chain P residue 33 LEU Chi-restraints excluded: chain P residue 68 GLU Chi-restraints excluded: chain P residue 100 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 32 optimal weight: 0.0770 chunk 17 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 44 optimal weight: 7.9990 chunk 36 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 49 optimal weight: 5.9990 chunk 28 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 chunk 25 optimal weight: 0.8980 chunk 3 optimal weight: 2.9990 overall best weight: 1.1944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... O 76 ASN O 93 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.168112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.137212 restraints weight = 9164.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.137562 restraints weight = 7875.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.138585 restraints weight = 7098.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.139081 restraints weight = 6226.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.139278 restraints weight = 5903.533| |-----------------------------------------------------------------------------| r_work (final): 0.3635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.3314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 5673 Z= 0.222 Angle : 0.692 12.752 7704 Z= 0.361 Chirality : 0.047 0.224 821 Planarity : 0.005 0.048 986 Dihedral : 5.118 23.404 772 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.43 % Allowed : 9.28 % Favored : 90.29 % Rotamer: Outliers : 6.05 % Allowed : 30.42 % Favored : 63.53 % 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: -0.54 (0.33), residues: 690 helix: None (None), residues: 0 sheet: 0.69 (0.33), residues: 270 loop : -1.13 (0.31), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG N 96 TYR 0.022 0.002 TYR N 49 PHE 0.038 0.002 PHE L 71 TRP 0.018 0.002 TRP O 47 HIS 0.007 0.001 HIS H 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00531 / 0.22 ( 5667) covalent geometry : angle 0.69026 / 0.36 ( 7692) SS BOND : bond 0.00621 / 0.41 ( 6) SS BOND : angle 1.39139 / 1.04 ( 12) hydrogen bonds : bond 0.03882 / 2.54 ( 181) hydrogen bonds : angle 5.55643 / 3.81 ( 456) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 131 time to evaluate : 0.216 Fit side-chains revert: symmetry clash REVERT: H 76 ASN cc_start: 0.7551 (m110) cc_final: 0.7333 (m-40) REVERT: M 85 GLU cc_start: 0.7727 (pm20) cc_final: 0.7338 (pm20) REVERT: M 94 ARG cc_start: 0.7481 (ttt180) cc_final: 0.7097 (ttt-90) REVERT: N 31 ARG cc_start: 0.7718 (mmm-85) cc_final: 0.6873 (tpt170) REVERT: N 79 GLN cc_start: 0.8332 (mt0) cc_final: 0.7949 (mm-40) REVERT: N 100 GLN cc_start: 0.7754 (tm-30) cc_final: 0.7481 (tm-30) REVERT: O 34 MET cc_start: 0.6788 (ptt) cc_final: 0.6434 (ptt) REVERT: O 43 LYS cc_start: 0.8894 (mptt) cc_final: 0.8679 (mmtp) REVERT: P 48 ILE cc_start: 0.8536 (mm) cc_final: 0.8215 (mm) REVERT: G 117 ASN cc_start: 0.8133 (m-40) cc_final: 0.7692 (m-40) outliers start: 36 outliers final: 30 residues processed: 154 average time/residue: 0.0690 time to fit residues: 14.0055 Evaluate side-chains 153 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 123 time to evaluate : 0.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 53 ASP Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain L residue 29 ILE Chi-restraints excluded: chain L residue 49 TYR Chi-restraints excluded: chain M residue 18 LEU Chi-restraints excluded: chain M residue 31 THR Chi-restraints excluded: chain M residue 51 ILE Chi-restraints excluded: chain M residue 62 SER Chi-restraints excluded: chain M residue 82 MET Chi-restraints excluded: chain M residue 107 THR Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 10 THR Chi-restraints excluded: chain N residue 19 VAL Chi-restraints excluded: chain N residue 49 TYR Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain O residue 6 GLU Chi-restraints excluded: chain O residue 28 ILE Chi-restraints excluded: chain O residue 29 PHE Chi-restraints excluded: chain O residue 62 SER Chi-restraints excluded: chain O residue 68 THR Chi-restraints excluded: chain O residue 82 SER Chi-restraints excluded: chain O residue 87 THR Chi-restraints excluded: chain O residue 107 THR Chi-restraints excluded: chain P residue 26 SER Chi-restraints excluded: chain P residue 33 LEU Chi-restraints excluded: chain P residue 68 GLU Chi-restraints excluded: chain P residue 100 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 64 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 25 optimal weight: 0.9990 chunk 59 optimal weight: 3.9990 chunk 24 optimal weight: 0.6980 chunk 4 optimal weight: 0.0570 chunk 3 optimal weight: 0.5980 chunk 18 optimal weight: 0.6980 chunk 8 optimal weight: 0.9980 chunk 5 optimal weight: 0.6980 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 13 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.171866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.140475 restraints weight = 9182.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.143372 restraints weight = 6773.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.145388 restraints weight = 5556.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.146530 restraints weight = 4844.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.147691 restraints weight = 4430.916| |-----------------------------------------------------------------------------| r_work (final): 0.3739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.3395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5673 Z= 0.141 Angle : 0.658 13.734 7704 Z= 0.339 Chirality : 0.046 0.164 821 Planarity : 0.004 0.047 986 Dihedral : 4.822 19.279 772 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.29 % Allowed : 7.68 % Favored : 92.03 % Rotamer: Outliers : 4.54 % Allowed : 31.43 % Favored : 64.03 % 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: -0.39 (0.33), residues: 690 helix: None (None), residues: 0 sheet: 0.94 (0.33), residues: 258 loop : -1.08 (0.31), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG O 19 TYR 0.020 0.002 TYR L 91 PHE 0.028 0.002 PHE L 71 TRP 0.035 0.002 TRP O 36 HIS 0.005 0.001 HIS H 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.14 ( 5667) covalent geometry : angle 0.65343 / 0.34 ( 7692) SS BOND : bond 0.00730 / 0.55 ( 6) SS BOND : angle 2.04288 / 1.35 ( 12) hydrogen bonds : bond 0.03532 / 2.22 ( 181) hydrogen bonds : angle 5.28937 / 3.63 ( 456) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 129 time to evaluate : 0.198 Fit side-chains REVERT: L 17 ASP cc_start: 0.8372 (t0) cc_final: 0.8163 (t0) REVERT: M 85 GLU cc_start: 0.7582 (pm20) cc_final: 0.7170 (pm20) REVERT: M 94 ARG cc_start: 0.7264 (ttt180) cc_final: 0.6520 (tpt-90) REVERT: N 31 ARG cc_start: 0.7644 (mmm-85) cc_final: 0.6838 (tpt170) REVERT: N 79 GLN cc_start: 0.8238 (mt0) cc_final: 0.7916 (mm-40) REVERT: N 100 GLN cc_start: 0.7740 (tm-30) cc_final: 0.7415 (tm-30) REVERT: O 43 LYS cc_start: 0.8874 (mptt) cc_final: 0.8645 (mmtp) REVERT: P 48 ILE cc_start: 0.8472 (mm) cc_final: 0.8210 (mm) REVERT: G 117 ASN cc_start: 0.8071 (m-40) cc_final: 0.7793 (m-40) outliers start: 27 outliers final: 23 residues processed: 146 average time/residue: 0.0703 time to fit residues: 13.6031 Evaluate side-chains 143 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 120 time to evaluate : 0.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 53 ASP Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain L residue 29 ILE Chi-restraints excluded: chain L residue 49 TYR Chi-restraints excluded: chain M residue 31 THR Chi-restraints excluded: chain M residue 51 ILE Chi-restraints excluded: chain M residue 107 THR Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 19 VAL Chi-restraints excluded: chain N residue 49 TYR Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain O residue 28 ILE Chi-restraints excluded: chain O residue 29 PHE Chi-restraints excluded: chain O residue 62 SER Chi-restraints excluded: chain O residue 82 SER Chi-restraints excluded: chain O residue 87 THR Chi-restraints excluded: chain P residue 26 SER Chi-restraints excluded: chain P residue 33 LEU Chi-restraints excluded: chain P residue 68 GLU Chi-restraints excluded: chain P residue 100 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 45 optimal weight: 1.9990 chunk 34 optimal weight: 5.9990 chunk 28 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 60 optimal weight: 0.8980 chunk 3 optimal weight: 0.7980 chunk 41 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 46 optimal weight: 0.6980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... M 13 GLN N 70 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.166478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.135913 restraints weight = 9163.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.136499 restraints weight = 7858.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.137461 restraints weight = 6666.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.137785 restraints weight = 6192.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.138083 restraints weight = 5772.739| |-----------------------------------------------------------------------------| r_work (final): 0.3622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.3616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 5673 Z= 0.233 Angle : 0.731 13.220 7704 Z= 0.377 Chirality : 0.048 0.368 821 Planarity : 0.005 0.046 986 Dihedral : 5.205 20.540 772 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 13.00 Ramachandran Plot: Outliers : 0.29 % Allowed : 9.57 % Favored : 90.14 % Rotamer: Outliers : 6.22 % Allowed : 29.58 % Favored : 64.20 % 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: -0.62 (0.33), residues: 690 helix: None (None), residues: 0 sheet: 0.82 (0.34), residues: 255 loop : -1.26 (0.31), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG N 96 TYR 0.020 0.002 TYR L 49 PHE 0.024 0.003 PHE H 67 TRP 0.043 0.003 TRP L 32 HIS 0.008 0.002 HIS O 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00554 / 0.23 ( 5667) covalent geometry : angle 0.72805 / 0.38 ( 7692) SS BOND : bond 0.00640 / 0.44 ( 6) SS BOND : angle 1.76504 / 1.23 ( 12) hydrogen bonds : bond 0.04255 / 2.70 ( 181) hydrogen bonds : angle 5.63327 / 3.83 ( 456) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 135 time to evaluate : 0.197 Fit side-chains revert: symmetry clash REVERT: L 17 ASP cc_start: 0.8470 (t0) cc_final: 0.8235 (t0) REVERT: M 30 THR cc_start: 0.8951 (m) cc_final: 0.8737 (p) REVERT: M 52 PHE cc_start: 0.5270 (OUTLIER) cc_final: 0.4846 (m-10) REVERT: M 85 GLU cc_start: 0.7737 (pm20) cc_final: 0.7353 (pm20) REVERT: M 94 ARG cc_start: 0.7433 (ttt180) cc_final: 0.6716 (tpt-90) REVERT: N 31 ARG cc_start: 0.7694 (mmm-85) cc_final: 0.7344 (mmm160) REVERT: N 79 GLN cc_start: 0.8362 (mt0) cc_final: 0.8006 (mm-40) REVERT: N 100 GLN cc_start: 0.7799 (tm-30) cc_final: 0.7566 (tm-30) REVERT: P 48 ILE cc_start: 0.8588 (mm) cc_final: 0.8256 (mm) REVERT: G 117 ASN cc_start: 0.8186 (m-40) cc_final: 0.7842 (m-40) outliers start: 37 outliers final: 27 residues processed: 157 average time/residue: 0.0689 time to fit residues: 14.6343 Evaluate side-chains 159 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 131 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 53 ASP Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain L residue 29 ILE Chi-restraints excluded: chain L residue 49 TYR Chi-restraints excluded: chain M residue 31 THR Chi-restraints excluded: chain M residue 51 ILE Chi-restraints excluded: chain M residue 52 PHE Chi-restraints excluded: chain M residue 107 THR Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 19 VAL Chi-restraints excluded: chain N residue 49 TYR Chi-restraints excluded: chain N residue 70 HIS Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain O residue 6 GLU Chi-restraints excluded: chain O residue 28 ILE Chi-restraints excluded: chain O residue 29 PHE Chi-restraints excluded: chain O residue 30 THR Chi-restraints excluded: chain O residue 62 SER Chi-restraints excluded: chain O residue 82 SER Chi-restraints excluded: chain O residue 87 THR Chi-restraints excluded: chain O residue 107 THR Chi-restraints excluded: chain P residue 26 SER Chi-restraints excluded: chain P residue 33 LEU Chi-restraints excluded: chain P residue 68 GLU Chi-restraints excluded: chain P residue 100 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 55 optimal weight: 0.5980 chunk 0 optimal weight: 3.9990 chunk 14 optimal weight: 0.7980 chunk 15 optimal weight: 0.6980 chunk 38 optimal weight: 6.9990 chunk 47 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 chunk 1 optimal weight: 3.9990 chunk 8 optimal weight: 0.0370 chunk 32 optimal weight: 0.9990 chunk 63 optimal weight: 0.0980 overall best weight: 0.4458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.172343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.141145 restraints weight = 9116.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.144145 restraints weight = 6686.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.146237 restraints weight = 5461.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.147459 restraints weight = 4753.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.148612 restraints weight = 4340.508| |-----------------------------------------------------------------------------| r_work (final): 0.3773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.3662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5673 Z= 0.135 Angle : 0.690 14.529 7704 Z= 0.354 Chirality : 0.046 0.196 821 Planarity : 0.005 0.047 986 Dihedral : 4.849 19.451 772 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.29 % Allowed : 7.25 % Favored : 92.46 % Rotamer: Outliers : 3.87 % Allowed : 33.28 % Favored : 62.86 % 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: -0.45 (0.34), residues: 690 helix: None (None), residues: 0 sheet: 0.92 (0.32), residues: 274 loop : -1.22 (0.32), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG N 96 TYR 0.019 0.002 TYR P 91 PHE 0.019 0.002 PHE H 67 TRP 0.043 0.002 TRP L 32 HIS 0.009 0.002 HIS N 70 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.13 ( 5667) covalent geometry : angle 0.68733 / 0.35 ( 7692) SS BOND : bond 0.00567 / 0.36 ( 6) SS BOND : angle 1.79022 / 1.21 ( 12) hydrogen bonds : bond 0.03629 / 2.25 ( 181) hydrogen bonds : angle 5.33189 / 3.63 ( 456) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 133 time to evaluate : 0.208 Fit side-chains revert: symmetry clash REVERT: L 17 ASP cc_start: 0.8410 (t0) cc_final: 0.8180 (t0) REVERT: M 85 GLU cc_start: 0.7639 (pm20) cc_final: 0.7242 (pm20) REVERT: M 94 ARG cc_start: 0.7115 (ttt180) cc_final: 0.6885 (tpt-90) REVERT: N 31 ARG cc_start: 0.7630 (mmm-85) cc_final: 0.6773 (tpt170) REVERT: N 79 GLN cc_start: 0.8258 (mt0) cc_final: 0.7969 (mm-40) REVERT: N 100 GLN cc_start: 0.7775 (tm-30) cc_final: 0.7489 (tm-30) REVERT: P 48 ILE cc_start: 0.8518 (mm) cc_final: 0.8256 (mm) REVERT: G 117 ASN cc_start: 0.8084 (m-40) cc_final: 0.7600 (m-40) outliers start: 23 outliers final: 20 residues processed: 148 average time/residue: 0.0604 time to fit residues: 12.1186 Evaluate side-chains 149 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 129 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 53 ASP Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain L residue 49 TYR Chi-restraints excluded: chain M residue 31 THR Chi-restraints excluded: chain M residue 51 ILE Chi-restraints excluded: chain M residue 107 THR Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 19 VAL Chi-restraints excluded: chain N residue 49 TYR Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain O residue 29 PHE Chi-restraints excluded: chain O residue 62 SER Chi-restraints excluded: chain O residue 87 THR Chi-restraints excluded: chain P residue 26 SER Chi-restraints excluded: chain P residue 33 LEU Chi-restraints excluded: chain P residue 68 GLU Chi-restraints excluded: chain P residue 100 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 32 optimal weight: 0.7980 chunk 22 optimal weight: 0.3980 chunk 20 optimal weight: 0.9980 chunk 48 optimal weight: 3.9990 chunk 42 optimal weight: 7.9990 chunk 54 optimal weight: 0.5980 chunk 5 optimal weight: 0.0770 chunk 16 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.171794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.140678 restraints weight = 9207.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.143697 restraints weight = 6798.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.145752 restraints weight = 5560.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.147082 restraints weight = 4847.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 15)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.147345 restraints weight = 4413.078| |-----------------------------------------------------------------------------| r_work (final): 0.3761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.3740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5673 Z= 0.147 Angle : 0.695 14.126 7704 Z= 0.356 Chirality : 0.047 0.308 821 Planarity : 0.005 0.047 986 Dihedral : 4.825 19.336 772 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.99 % Favored : 90.87 % Rotamer: Outliers : 3.70 % Allowed : 33.78 % Favored : 62.52 % 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: -0.43 (0.34), residues: 690 helix: None (None), residues: 0 sheet: 0.84 (0.32), residues: 274 loop : -1.13 (0.33), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG O 19 TYR 0.020 0.002 TYR N 94 PHE 0.028 0.002 PHE O 52A TRP 0.043 0.002 TRP L 32 HIS 0.005 0.001 HIS H 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.15 ( 5667) covalent geometry : angle 0.69174 / 0.35 ( 7692) SS BOND : bond 0.00622 / 0.42 ( 6) SS BOND : angle 1.75771 / 1.19 ( 12) hydrogen bonds : bond 0.03572 / 2.25 ( 181) hydrogen bonds : angle 5.29474 / 3.60 ( 456) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 127 time to evaluate : 0.209 Fit side-chains revert: symmetry clash REVERT: L 65 SER cc_start: 0.8785 (t) cc_final: 0.8529 (m) REVERT: M 85 GLU cc_start: 0.7677 (pm20) cc_final: 0.7253 (pm20) REVERT: N 31 ARG cc_start: 0.7644 (mmm-85) cc_final: 0.6802 (tpt170) REVERT: N 79 GLN cc_start: 0.8281 (mt0) cc_final: 0.8009 (mm-40) REVERT: N 100 GLN cc_start: 0.7782 (tm-30) cc_final: 0.7495 (tm-30) REVERT: P 48 ILE cc_start: 0.8505 (mm) cc_final: 0.8218 (mm) outliers start: 22 outliers final: 20 residues processed: 140 average time/residue: 0.0624 time to fit residues: 11.8832 Evaluate side-chains 144 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 124 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 53 ASP Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain L residue 49 TYR Chi-restraints excluded: chain M residue 31 THR Chi-restraints excluded: chain M residue 51 ILE Chi-restraints excluded: chain M residue 107 THR Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 19 VAL Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain O residue 29 PHE Chi-restraints excluded: chain O residue 62 SER Chi-restraints excluded: chain O residue 68 THR Chi-restraints excluded: chain O residue 87 THR Chi-restraints excluded: chain P residue 26 SER Chi-restraints excluded: chain P residue 33 LEU Chi-restraints excluded: chain P residue 68 GLU Chi-restraints excluded: chain P residue 100 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 54 optimal weight: 0.1980 chunk 58 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 56 optimal weight: 0.6980 chunk 5 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 38 optimal weight: 7.9990 chunk 12 optimal weight: 0.8980 chunk 18 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... N 70 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.155595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.120769 restraints weight = 8396.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.123792 restraints weight = 5933.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.125983 restraints weight = 4725.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.127317 restraints weight = 4060.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.128537 restraints weight = 3671.484| |-----------------------------------------------------------------------------| r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.3846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 5673 Z= 0.162 Angle : 0.698 13.917 7704 Z= 0.359 Chirality : 0.046 0.219 821 Planarity : 0.004 0.047 986 Dihedral : 4.886 19.523 772 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.29 % Allowed : 8.55 % Favored : 91.16 % Rotamer: Outliers : 3.87 % Allowed : 33.28 % Favored : 62.86 % 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: -0.55 (0.34), residues: 690 helix: None (None), residues: 0 sheet: 0.75 (0.32), residues: 274 loop : -1.20 (0.32), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG O 19 TYR 0.024 0.002 TYR N 94 PHE 0.022 0.002 PHE O 27 TRP 0.044 0.002 TRP L 32 HIS 0.006 0.001 HIS H 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.16 ( 5667) covalent geometry : angle 0.69490 / 0.36 ( 7692) SS BOND : bond 0.00605 / 0.39 ( 6) SS BOND : angle 1.75432 / 1.19 ( 12) hydrogen bonds : bond 0.03749 / 2.36 ( 181) hydrogen bonds : angle 5.32478 / 3.62 ( 456) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1111.33 seconds wall clock time: 19 minutes 51.37 seconds (1191.37 seconds total)