Starting phenix.real_space_refine on Tue Aug 4 12:36:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9o9k_70253/08_2026/9o9k_70253.cif Found real_map, /net/cci-nas-00/data/ceres_data/9o9k_70253/08_2026/9o9k_70253.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9o9k_70253/08_2026/9o9k_70253.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9o9k_70253/08_2026/9o9k_70253.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9o9k_70253/08_2026/9o9k_70253.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9o9k_70253/08_2026/9o9k_70253.map" } resolution = 2.9 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= 0.006 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: 3 Type Number sf(0) Gaussians C 1760 2.51 5 N 500 2.21 5 O 625 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 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: 2885 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 487 Classifications: {'peptide': 70} Link IDs: {'TRANS': 69} Chain: "B" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 45 Classifications: {'peptide': 9} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'UNK:plan-1': 9} Unresolved non-hydrogen planarities: 9 Chain: "C" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 35 Classifications: {'peptide': 7} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'TRANS': 6} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'UNK:plan-1': 7} Unresolved non-hydrogen planarities: 7 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: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "F" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "L" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "M" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "N" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "O" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Restraints were copied for chains: D, G, J, M, E, H, K, N, F, I, L, O Time building chain proxies: 0.64, per 1000 atoms: 0.22 Number of scatterers: 2885 At special positions: 0 Unit cell: (88.6772, 64.592, 40.5069, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 625 8.00 N 500 7.00 C 1760 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.21 Conformation dependent library (CDL) restraints added in 106.0 milliseconds 680 Ramachandran restraints generated. 340 Oldfield, 0 Emsley, 340 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 750 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 0 helices and 0 sheets defined 0.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... No hydrogen bonds 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: 0.00 Time building geometry restraints manager: 0.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.27: 515 1.27 - 1.34: 395 1.34 - 1.41: 110 1.41 - 1.47: 520 1.47 - 1.54: 1290 Bond restraints: 2830 Sorted by residual: bond pdb=" CA ALA M 85 " pdb=" CB ALA M 85 " ideal model delta sigma weight residual 1.532 1.486 0.046 1.62e-02 3.81e+03 8.03e+00 bond pdb=" CA ALA G 85 " pdb=" CB ALA G 85 " ideal model delta sigma weight residual 1.532 1.487 0.046 1.62e-02 3.81e+03 7.97e+00 bond pdb=" CA ALA D 85 " pdb=" CB ALA D 85 " ideal model delta sigma weight residual 1.532 1.487 0.046 1.62e-02 3.81e+03 7.96e+00 bond pdb=" CA ALA A 85 " pdb=" CB ALA A 85 " ideal model delta sigma weight residual 1.532 1.487 0.045 1.62e-02 3.81e+03 7.86e+00 bond pdb=" CA ALA J 85 " pdb=" CB ALA J 85 " ideal model delta sigma weight residual 1.532 1.488 0.045 1.62e-02 3.81e+03 7.64e+00 ... (remaining 2825 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.93: 3085 1.93 - 3.86: 600 3.86 - 5.78: 100 5.78 - 7.71: 20 7.71 - 9.64: 10 Bond angle restraints: 3815 Sorted by residual: angle pdb=" CA THR M 72 " pdb=" CB THR M 72 " pdb=" OG1 THR M 72 " ideal model delta sigma weight residual 109.60 99.96 9.64 1.50e+00 4.44e-01 4.13e+01 angle pdb=" CA THR G 72 " pdb=" CB THR G 72 " pdb=" OG1 THR G 72 " ideal model delta sigma weight residual 109.60 99.97 9.63 1.50e+00 4.44e-01 4.12e+01 angle pdb=" CA THR A 72 " pdb=" CB THR A 72 " pdb=" OG1 THR A 72 " ideal model delta sigma weight residual 109.60 99.97 9.63 1.50e+00 4.44e-01 4.12e+01 angle pdb=" CA THR D 72 " pdb=" CB THR D 72 " pdb=" OG1 THR D 72 " ideal model delta sigma weight residual 109.60 99.97 9.63 1.50e+00 4.44e-01 4.12e+01 angle pdb=" CA THR J 72 " pdb=" CB THR J 72 " pdb=" OG1 THR J 72 " ideal model delta sigma weight residual 109.60 99.98 9.62 1.50e+00 4.44e-01 4.12e+01 ... (remaining 3810 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 1620 17.93 - 35.87: 40 35.87 - 53.80: 0 53.80 - 71.73: 10 71.73 - 89.66: 10 Dihedral angle restraints: 1680 sinusoidal: 510 harmonic: 1170 Sorted by residual: dihedral pdb=" CB GLU D 57 " pdb=" CG GLU D 57 " pdb=" CD GLU D 57 " pdb=" OE1 GLU D 57 " ideal model delta sinusoidal sigma weight residual 0.00 81.77 -81.77 1 3.00e+01 1.11e-03 9.14e+00 dihedral pdb=" CB GLU J 57 " pdb=" CG GLU J 57 " pdb=" CD GLU J 57 " pdb=" OE1 GLU J 57 " ideal model delta sinusoidal sigma weight residual 0.00 81.77 -81.77 1 3.00e+01 1.11e-03 9.14e+00 dihedral pdb=" CB GLU A 57 " pdb=" CG GLU A 57 " pdb=" CD GLU A 57 " pdb=" OE1 GLU A 57 " ideal model delta sinusoidal sigma weight residual 0.00 81.76 -81.76 1 3.00e+01 1.11e-03 9.14e+00 ... (remaining 1677 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 289 0.058 - 0.117: 176 0.117 - 0.175: 35 0.175 - 0.233: 0 0.233 - 0.291: 5 Chirality restraints: 505 Sorted by residual: chirality pdb=" CA VAL J 71 " pdb=" N VAL J 71 " pdb=" C VAL J 71 " pdb=" CB VAL J 71 " both_signs ideal model delta sigma weight residual False 2.44 2.73 -0.29 2.00e-01 2.50e+01 2.12e+00 chirality pdb=" CA VAL A 71 " pdb=" N VAL A 71 " pdb=" C VAL A 71 " pdb=" CB VAL A 71 " both_signs ideal model delta sigma weight residual False 2.44 2.73 -0.29 2.00e-01 2.50e+01 2.12e+00 chirality pdb=" CA VAL D 71 " pdb=" N VAL D 71 " pdb=" C VAL D 71 " pdb=" CB VAL D 71 " both_signs ideal model delta sigma weight residual False 2.44 2.73 -0.29 2.00e-01 2.50e+01 2.12e+00 ... (remaining 502 not shown) Planarity restraints: 480 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR D 39 " 0.034 2.00e-02 2.50e+03 1.92e-02 7.40e+00 pdb=" CG TYR D 39 " -0.034 2.00e-02 2.50e+03 pdb=" CD1 TYR D 39 " -0.017 2.00e-02 2.50e+03 pdb=" CD2 TYR D 39 " -0.010 2.00e-02 2.50e+03 pdb=" CE1 TYR D 39 " 0.009 2.00e-02 2.50e+03 pdb=" CE2 TYR D 39 " 0.003 2.00e-02 2.50e+03 pdb=" CZ TYR D 39 " 0.011 2.00e-02 2.50e+03 pdb=" OH TYR D 39 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR J 39 " 0.034 2.00e-02 2.50e+03 1.92e-02 7.38e+00 pdb=" CG TYR J 39 " -0.034 2.00e-02 2.50e+03 pdb=" CD1 TYR J 39 " -0.017 2.00e-02 2.50e+03 pdb=" CD2 TYR J 39 " -0.010 2.00e-02 2.50e+03 pdb=" CE1 TYR J 39 " 0.009 2.00e-02 2.50e+03 pdb=" CE2 TYR J 39 " 0.003 2.00e-02 2.50e+03 pdb=" CZ TYR J 39 " 0.011 2.00e-02 2.50e+03 pdb=" OH TYR J 39 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR M 39 " 0.034 2.00e-02 2.50e+03 1.92e-02 7.37e+00 pdb=" CG TYR M 39 " -0.034 2.00e-02 2.50e+03 pdb=" CD1 TYR M 39 " -0.017 2.00e-02 2.50e+03 pdb=" CD2 TYR M 39 " -0.010 2.00e-02 2.50e+03 pdb=" CE1 TYR M 39 " 0.009 2.00e-02 2.50e+03 pdb=" CE2 TYR M 39 " 0.003 2.00e-02 2.50e+03 pdb=" CZ TYR M 39 " 0.011 2.00e-02 2.50e+03 pdb=" OH TYR M 39 " 0.003 2.00e-02 2.50e+03 ... (remaining 477 not shown) Histogram of nonbonded interaction distances: 2.45 - 2.94: 1310 2.94 - 3.43: 2692 3.43 - 3.92: 4337 3.92 - 4.41: 5467 4.41 - 4.90: 10193 Nonbonded interactions: 23999 Sorted by model distance: nonbonded pdb=" OG1 THR D 75 " pdb=" OG1 THR G 92 " model vdw 2.450 3.040 nonbonded pdb=" OG1 THR A 75 " pdb=" OG1 THR J 92 " model vdw 2.451 3.040 nonbonded pdb=" OG1 THR J 75 " pdb=" OG1 THR M 92 " model vdw 2.451 3.040 nonbonded pdb=" OG1 THR A 92 " pdb=" OG1 THR G 75 " model vdw 2.451 3.040 nonbonded pdb=" N THR D 59 " pdb=" OG1 THR D 59 " model vdw 2.590 2.496 ... (remaining 23994 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' selection = chain 'G' selection = chain 'J' selection = chain 'M' } ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'H' selection = chain 'K' selection = chain 'N' } ncs_group { reference = chain 'C' selection = chain 'F' selection = chain 'I' selection = chain 'L' selection = chain 'O' } 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: 0.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.050 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 4.110 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 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 : 0.011 0.053 2830 Z= 0.677 Angle : 1.691 9.641 3815 Z= 1.029 Chirality : 0.072 0.291 505 Planarity : 0.007 0.021 480 Dihedral : 13.891 89.663 930 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.24 % Favored : 86.76 % Rotamer: Outliers : 2.00 % Allowed : 0.00 % Favored : 98.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.29 (0.25), residues: 340 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.02 (0.19), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.034 0.015 TYR J 39 PHE 0.013 0.007 PHE D 94 Details of bonding type rmsd/Z covalent geometry : bond 0.01101 / 0.68 ( 2830) covalent geometry : angle 1.69127 / 1.03 ( 3815) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 680 Ramachandran restraints generated. 340 Oldfield, 0 Emsley, 340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 680 Ramachandran restraints generated. 340 Oldfield, 0 Emsley, 340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 42 time to evaluate : 0.061 Fit side-chains REVERT: A 32 LYS cc_start: 0.8319 (mttt) cc_final: 0.7987 (mtpt) REVERT: A 34 LYS cc_start: 0.8579 (mttt) cc_final: 0.8369 (mttp) REVERT: D 32 LYS cc_start: 0.8377 (mttt) cc_final: 0.7851 (mtpt) REVERT: G 32 LYS cc_start: 0.8417 (mttt) cc_final: 0.7994 (mtpt) REVERT: G 44 THR cc_start: 0.9181 (t) cc_final: 0.8884 (p) REVERT: G 83 GLU cc_start: 0.8707 (mt-10) cc_final: 0.8355 (tt0) REVERT: J 32 LYS cc_start: 0.8478 (mttt) cc_final: 0.8021 (mtpt) REVERT: J 38 LEU cc_start: 0.9154 (OUTLIER) cc_final: 0.8912 (pp) REVERT: M 32 LYS cc_start: 0.8764 (mttt) cc_final: 0.8477 (mtmt) REVERT: M 44 THR cc_start: 0.9214 (t) cc_final: 0.8856 (p) outliers start: 5 outliers final: 3 residues processed: 47 average time/residue: 0.5215 time to fit residues: 25.0907 Evaluate side-chains 36 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 32 time to evaluate : 0.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain G residue 38 LEU Chi-restraints excluded: chain J residue 38 LEU Chi-restraints excluded: chain M residue 38 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 24 optimal weight: 3.9990 chunk 26 optimal weight: 5.9990 chunk 2 optimal weight: 8.9990 chunk 16 optimal weight: 3.9990 chunk 32 optimal weight: 6.9990 chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 chunk 30 optimal weight: 6.9990 chunk 22 optimal weight: 0.8980 chunk 13 optimal weight: 5.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 62 GLN J 62 GLN M 62 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.117594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.099831 restraints weight = 3213.557| |-----------------------------------------------------------------------------| r_work (start): 0.3675 rms_B_bonded: 2.10 r_work: 0.3549 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3427 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.1659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.017 2830 Z= 0.175 Angle : 0.554 6.701 3815 Z= 0.284 Chirality : 0.050 0.129 505 Planarity : 0.002 0.006 480 Dihedral : 5.598 39.968 428 Min Nonbonded Distance : 2.649 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 1.60 % Allowed : 6.00 % Favored : 92.40 % 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: -4.45 (0.33), residues: 340 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.38 (0.25), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.013 0.003 TYR G 39 PHE 0.004 0.001 PHE J 94 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.17 ( 2830) covalent geometry : angle 0.55390 / 0.28 ( 3815) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 680 Ramachandran restraints generated. 340 Oldfield, 0 Emsley, 340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 680 Ramachandran restraints generated. 340 Oldfield, 0 Emsley, 340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 38 time to evaluate : 0.108 Fit side-chains REVERT: A 32 LYS cc_start: 0.8216 (mttt) cc_final: 0.7768 (mtpt) REVERT: A 38 LEU cc_start: 0.9008 (OUTLIER) cc_final: 0.8775 (pp) REVERT: D 32 LYS cc_start: 0.8457 (mttt) cc_final: 0.8041 (mtpm) REVERT: G 32 LYS cc_start: 0.8339 (mttt) cc_final: 0.7855 (mtpt) REVERT: J 32 LYS cc_start: 0.8587 (mttt) cc_final: 0.8071 (mtpt) REVERT: M 32 LYS cc_start: 0.8936 (mttt) cc_final: 0.8519 (mtmt) REVERT: M 42 SER cc_start: 0.9350 (p) cc_final: 0.9048 (p) outliers start: 4 outliers final: 0 residues processed: 41 average time/residue: 0.5664 time to fit residues: 23.8555 Evaluate side-chains 37 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 36 time to evaluate : 0.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 25 optimal weight: 9.9990 chunk 21 optimal weight: 10.0000 chunk 30 optimal weight: 7.9990 chunk 19 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 chunk 8 optimal weight: 10.0000 chunk 18 optimal weight: 2.9990 chunk 22 optimal weight: 9.9990 chunk 24 optimal weight: 3.9990 chunk 32 optimal weight: 0.0870 chunk 15 optimal weight: 3.9990 overall best weight: 1.9764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 50 GLN M 50 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.119679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.102330 restraints weight = 3202.515| |-----------------------------------------------------------------------------| r_work (start): 0.3727 rms_B_bonded: 2.13 r_work: 0.3604 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3482 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.2114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 2830 Z= 0.126 Angle : 0.434 6.436 3815 Z= 0.229 Chirality : 0.047 0.123 505 Planarity : 0.001 0.005 480 Dihedral : 3.365 9.963 420 Min Nonbonded Distance : 2.647 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 2.00 % Allowed : 10.00 % Favored : 88.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.23 (0.35), residues: 340 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.22 (0.27), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.012 0.003 TYR G 39 PHE 0.002 0.001 PHE J 94 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.13 ( 2830) covalent geometry : angle 0.43441 / 0.23 ( 3815) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 680 Ramachandran restraints generated. 340 Oldfield, 0 Emsley, 340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 680 Ramachandran restraints generated. 340 Oldfield, 0 Emsley, 340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 39 time to evaluate : 0.063 Fit side-chains REVERT: A 32 LYS cc_start: 0.8170 (mttt) cc_final: 0.7706 (mtpt) REVERT: D 32 LYS cc_start: 0.8442 (mttt) cc_final: 0.8072 (mtmt) REVERT: G 32 LYS cc_start: 0.8338 (mttt) cc_final: 0.7920 (mtmt) REVERT: J 32 LYS cc_start: 0.8517 (mttt) cc_final: 0.8081 (mtpt) REVERT: J 42 SER cc_start: 0.9160 (p) cc_final: 0.8881 (p) REVERT: M 32 LYS cc_start: 0.8937 (mttt) cc_final: 0.8512 (mtmt) REVERT: M 42 SER cc_start: 0.9355 (p) cc_final: 0.9015 (p) outliers start: 5 outliers final: 0 residues processed: 44 average time/residue: 0.4101 time to fit residues: 18.4946 Evaluate side-chains 39 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 39 time to evaluate : 0.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 15 optimal weight: 9.9990 chunk 1 optimal weight: 2.9990 chunk 34 optimal weight: 4.9990 chunk 20 optimal weight: 9.9990 chunk 9 optimal weight: 6.9990 chunk 31 optimal weight: 9.9990 chunk 27 optimal weight: 5.9990 chunk 11 optimal weight: 0.8980 chunk 28 optimal weight: 9.9990 chunk 16 optimal weight: 0.9990 chunk 2 optimal weight: 5.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 50 GLN M 50 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.115665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.098524 restraints weight = 3195.924| |-----------------------------------------------------------------------------| r_work (start): 0.3666 rms_B_bonded: 2.05 r_work: 0.3541 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3419 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.2183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 2830 Z= 0.187 Angle : 0.495 7.861 3815 Z= 0.256 Chirality : 0.048 0.126 505 Planarity : 0.001 0.006 480 Dihedral : 3.675 10.903 420 Min Nonbonded Distance : 2.640 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 1.60 % Allowed : 10.80 % Favored : 87.60 % 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: -4.15 (0.36), residues: 340 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.15 (0.27), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.013 0.003 TYR G 39 PHE 0.003 0.001 PHE J 94 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.19 ( 2830) covalent geometry : angle 0.49451 / 0.26 ( 3815) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 680 Ramachandran restraints generated. 340 Oldfield, 0 Emsley, 340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 680 Ramachandran restraints generated. 340 Oldfield, 0 Emsley, 340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 37 time to evaluate : 0.056 Fit side-chains REVERT: A 32 LYS cc_start: 0.8196 (mttt) cc_final: 0.7716 (mtpt) REVERT: D 32 LYS cc_start: 0.8436 (mttt) cc_final: 0.7912 (mtpp) REVERT: G 32 LYS cc_start: 0.8300 (mttt) cc_final: 0.7888 (mtmt) REVERT: G 38 LEU cc_start: 0.9056 (OUTLIER) cc_final: 0.8659 (pp) REVERT: J 32 LYS cc_start: 0.8542 (mttt) cc_final: 0.8072 (mtpt) REVERT: J 42 SER cc_start: 0.9172 (p) cc_final: 0.8905 (p) REVERT: M 32 LYS cc_start: 0.8816 (mttt) cc_final: 0.8446 (mtmt) outliers start: 4 outliers final: 0 residues processed: 41 average time/residue: 0.3940 time to fit residues: 16.5735 Evaluate side-chains 38 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 37 time to evaluate : 0.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 38 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 28 optimal weight: 7.9990 chunk 16 optimal weight: 20.0000 chunk 18 optimal weight: 10.0000 chunk 11 optimal weight: 0.8980 chunk 32 optimal weight: 0.9980 chunk 25 optimal weight: 0.8980 chunk 20 optimal weight: 9.9990 chunk 6 optimal weight: 7.9990 chunk 10 optimal weight: 2.9990 chunk 7 optimal weight: 8.9990 chunk 9 optimal weight: 8.9990 overall best weight: 2.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... M 50 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.117169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.100096 restraints weight = 3138.559| |-----------------------------------------------------------------------------| r_work (start): 0.3705 rms_B_bonded: 2.08 r_work: 0.3583 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3460 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.2340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2830 Z= 0.162 Angle : 0.449 6.502 3815 Z= 0.235 Chirality : 0.048 0.123 505 Planarity : 0.001 0.005 480 Dihedral : 3.531 10.561 420 Min Nonbonded Distance : 2.652 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.60 % Allowed : 12.40 % Favored : 86.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.00 (0.37), residues: 340 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.04 (0.28), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.012 0.003 TYR G 39 PHE 0.003 0.001 PHE G 94 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.16 ( 2830) covalent geometry : angle 0.44895 / 0.23 ( 3815) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 680 Ramachandran restraints generated. 340 Oldfield, 0 Emsley, 340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 680 Ramachandran restraints generated. 340 Oldfield, 0 Emsley, 340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 39 time to evaluate : 0.059 Fit side-chains REVERT: A 32 LYS cc_start: 0.8207 (mttt) cc_final: 0.7712 (mtpt) REVERT: D 32 LYS cc_start: 0.8435 (mttt) cc_final: 0.7904 (mtpp) REVERT: G 32 LYS cc_start: 0.8227 (mttt) cc_final: 0.7904 (mtmt) REVERT: G 38 LEU cc_start: 0.9110 (OUTLIER) cc_final: 0.8739 (pp) REVERT: G 83 GLU cc_start: 0.8275 (mt-10) cc_final: 0.8059 (tt0) REVERT: J 32 LYS cc_start: 0.8551 (mttt) cc_final: 0.8071 (mtpt) REVERT: J 42 SER cc_start: 0.9171 (p) cc_final: 0.8913 (p) REVERT: M 32 LYS cc_start: 0.8768 (mttt) cc_final: 0.8426 (mtmt) outliers start: 4 outliers final: 0 residues processed: 42 average time/residue: 0.4266 time to fit residues: 18.3551 Evaluate side-chains 40 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 39 time to evaluate : 0.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 38 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 2 optimal weight: 20.0000 chunk 20 optimal weight: 10.0000 chunk 32 optimal weight: 0.0670 chunk 8 optimal weight: 10.0000 chunk 19 optimal weight: 9.9990 chunk 18 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 3 optimal weight: 9.9990 chunk 10 optimal weight: 4.9990 chunk 17 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 overall best weight: 2.6126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... M 50 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.116880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.099588 restraints weight = 3258.119| |-----------------------------------------------------------------------------| r_work (start): 0.3701 rms_B_bonded: 2.15 r_work: 0.3575 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3450 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.2399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2830 Z= 0.156 Angle : 0.444 6.402 3815 Z= 0.232 Chirality : 0.047 0.125 505 Planarity : 0.001 0.005 480 Dihedral : 3.536 10.749 420 Min Nonbonded Distance : 2.649 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.60 % Allowed : 13.20 % Favored : 85.20 % 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: -3.93 (0.38), residues: 340 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.99 (0.29), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.012 0.003 TYR G 39 PHE 0.003 0.001 PHE M 94 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.16 ( 2830) covalent geometry : angle 0.44360 / 0.23 ( 3815) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 680 Ramachandran restraints generated. 340 Oldfield, 0 Emsley, 340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 680 Ramachandran restraints generated. 340 Oldfield, 0 Emsley, 340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 39 time to evaluate : 0.102 Fit side-chains REVERT: A 32 LYS cc_start: 0.8100 (mttt) cc_final: 0.7731 (mtpt) REVERT: D 32 LYS cc_start: 0.8421 (mttt) cc_final: 0.7882 (mtpp) REVERT: G 32 LYS cc_start: 0.8194 (mttt) cc_final: 0.7878 (mtmt) REVERT: G 38 LEU cc_start: 0.9107 (OUTLIER) cc_final: 0.8753 (pp) REVERT: G 83 GLU cc_start: 0.8334 (mt-10) cc_final: 0.8079 (tt0) REVERT: J 32 LYS cc_start: 0.8493 (mttt) cc_final: 0.7994 (mtpt) REVERT: J 42 SER cc_start: 0.9178 (p) cc_final: 0.8915 (p) REVERT: M 32 LYS cc_start: 0.8713 (mttt) cc_final: 0.8375 (mtmt) outliers start: 4 outliers final: 0 residues processed: 43 average time/residue: 0.3728 time to fit residues: 16.4727 Evaluate side-chains 40 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 39 time to evaluate : 0.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 38 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 19 optimal weight: 10.0000 chunk 32 optimal weight: 0.0470 chunk 2 optimal weight: 20.0000 chunk 25 optimal weight: 0.5980 chunk 27 optimal weight: 5.9990 chunk 7 optimal weight: 8.9990 chunk 14 optimal weight: 7.9990 chunk 10 optimal weight: 0.0980 chunk 22 optimal weight: 9.9990 chunk 5 optimal weight: 4.9990 chunk 9 optimal weight: 9.9990 overall best weight: 2.3482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... M 50 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.117759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.100696 restraints weight = 3216.681| |-----------------------------------------------------------------------------| r_work (start): 0.3727 rms_B_bonded: 2.11 r_work: 0.3602 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3480 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.2486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 2830 Z= 0.142 Angle : 0.429 6.033 3815 Z= 0.225 Chirality : 0.047 0.124 505 Planarity : 0.001 0.005 480 Dihedral : 3.462 10.304 420 Min Nonbonded Distance : 2.655 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.60 % Allowed : 13.20 % Favored : 85.20 % 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: -3.88 (0.38), residues: 340 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.95 (0.29), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.011 0.002 TYR G 39 PHE 0.003 0.001 PHE J 94 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.14 ( 2830) covalent geometry : angle 0.42890 / 0.22 ( 3815) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 680 Ramachandran restraints generated. 340 Oldfield, 0 Emsley, 340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 680 Ramachandran restraints generated. 340 Oldfield, 0 Emsley, 340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 42 time to evaluate : 0.059 Fit side-chains REVERT: A 32 LYS cc_start: 0.8073 (mttt) cc_final: 0.7716 (mtpt) REVERT: D 32 LYS cc_start: 0.8407 (mttt) cc_final: 0.8002 (mtmt) REVERT: G 32 LYS cc_start: 0.8166 (mttt) cc_final: 0.7845 (mtmt) REVERT: G 38 LEU cc_start: 0.9101 (OUTLIER) cc_final: 0.8748 (pp) REVERT: J 32 LYS cc_start: 0.8424 (mttt) cc_final: 0.7909 (mtpt) REVERT: J 42 SER cc_start: 0.9182 (p) cc_final: 0.8920 (p) REVERT: M 32 LYS cc_start: 0.8707 (mttt) cc_final: 0.8360 (mtmt) outliers start: 4 outliers final: 1 residues processed: 45 average time/residue: 0.3900 time to fit residues: 18.0320 Evaluate side-chains 43 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 41 time to evaluate : 0.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 38 LEU Chi-restraints excluded: chain J residue 38 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 25 optimal weight: 10.0000 chunk 29 optimal weight: 0.9990 chunk 11 optimal weight: 0.0770 chunk 20 optimal weight: 10.0000 chunk 32 optimal weight: 5.9990 chunk 13 optimal weight: 8.9990 chunk 28 optimal weight: 5.9990 chunk 33 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 1 optimal weight: 8.9990 chunk 15 optimal weight: 5.9990 overall best weight: 2.8146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... M 50 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.115880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.098466 restraints weight = 3297.578| |-----------------------------------------------------------------------------| r_work (start): 0.3693 rms_B_bonded: 2.17 r_work: 0.3570 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3445 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.2485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 2830 Z= 0.166 Angle : 0.460 5.977 3815 Z= 0.240 Chirality : 0.048 0.126 505 Planarity : 0.001 0.005 480 Dihedral : 3.629 11.294 420 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.60 % Allowed : 13.60 % Favored : 84.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.88 (0.37), residues: 340 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.95 (0.29), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.012 0.003 TYR M 39 PHE 0.003 0.001 PHE M 94 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.17 ( 2830) covalent geometry : angle 0.45984 / 0.24 ( 3815) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 680 Ramachandran restraints generated. 340 Oldfield, 0 Emsley, 340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 680 Ramachandran restraints generated. 340 Oldfield, 0 Emsley, 340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 41 time to evaluate : 0.090 Fit side-chains REVERT: A 32 LYS cc_start: 0.8091 (mttt) cc_final: 0.7732 (mtpt) REVERT: D 32 LYS cc_start: 0.8404 (mttt) cc_final: 0.7855 (mtpp) REVERT: G 32 LYS cc_start: 0.8174 (mttt) cc_final: 0.7854 (mtmt) REVERT: G 38 LEU cc_start: 0.9097 (OUTLIER) cc_final: 0.8733 (pp) REVERT: J 32 LYS cc_start: 0.8428 (mttt) cc_final: 0.7894 (mtpt) REVERT: J 42 SER cc_start: 0.9193 (p) cc_final: 0.8937 (p) REVERT: M 32 LYS cc_start: 0.8693 (mttt) cc_final: 0.8346 (mtmt) outliers start: 4 outliers final: 2 residues processed: 44 average time/residue: 0.3717 time to fit residues: 16.8047 Evaluate side-chains 44 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 41 time to evaluate : 0.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain G residue 38 LEU Chi-restraints excluded: chain J residue 38 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 23 optimal weight: 10.0000 chunk 28 optimal weight: 5.9990 chunk 15 optimal weight: 9.9990 chunk 1 optimal weight: 9.9990 chunk 27 optimal weight: 10.0000 chunk 16 optimal weight: 10.0000 chunk 29 optimal weight: 9.9990 chunk 25 optimal weight: 0.9980 chunk 30 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 17 optimal weight: 9.9990 overall best weight: 7.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... M 50 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.117263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.099108 restraints weight = 3271.371| |-----------------------------------------------------------------------------| r_work (start): 0.3666 rms_B_bonded: 2.10 r_work: 0.3552 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3430 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.2441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.047 2830 Z= 0.387 Angle : 0.709 7.077 3815 Z= 0.364 Chirality : 0.054 0.137 505 Planarity : 0.003 0.008 480 Dihedral : 4.628 13.977 420 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 1.60 % Allowed : 14.40 % Favored : 84.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.06 (0.37), residues: 340 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.09 (0.28), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.017 0.004 TYR G 39 PHE 0.004 0.001 PHE M 94 Details of bonding type rmsd/Z covalent geometry : bond 0.00837 / 0.39 ( 2830) covalent geometry : angle 0.70893 / 0.36 ( 3815) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 680 Ramachandran restraints generated. 340 Oldfield, 0 Emsley, 340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 680 Ramachandran restraints generated. 340 Oldfield, 0 Emsley, 340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 38 time to evaluate : 0.057 Fit side-chains REVERT: A 32 LYS cc_start: 0.8283 (mttt) cc_final: 0.8020 (mtpt) REVERT: D 32 LYS cc_start: 0.8518 (mttt) cc_final: 0.8010 (mtpp) REVERT: G 32 LYS cc_start: 0.8393 (mttt) cc_final: 0.8041 (mtmt) REVERT: G 38 LEU cc_start: 0.9119 (OUTLIER) cc_final: 0.8806 (pp) REVERT: J 32 LYS cc_start: 0.8646 (mttt) cc_final: 0.8149 (mtpt) REVERT: J 42 SER cc_start: 0.9197 (p) cc_final: 0.8976 (p) REVERT: M 32 LYS cc_start: 0.8669 (mttt) cc_final: 0.8400 (mtmt) outliers start: 4 outliers final: 3 residues processed: 41 average time/residue: 0.4004 time to fit residues: 16.8191 Evaluate side-chains 41 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 37 time to evaluate : 0.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain G residue 38 LEU Chi-restraints excluded: chain J residue 38 LEU Chi-restraints excluded: chain M residue 75 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 17 optimal weight: 0.9980 chunk 34 optimal weight: 6.9990 chunk 5 optimal weight: 7.9990 chunk 18 optimal weight: 1.9990 chunk 1 optimal weight: 5.9990 chunk 30 optimal weight: 6.9990 chunk 29 optimal weight: 0.9980 chunk 16 optimal weight: 6.9990 chunk 24 optimal weight: 0.9980 chunk 27 optimal weight: 6.9990 chunk 11 optimal weight: 8.9990 overall best weight: 2.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... M 50 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.118264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.100314 restraints weight = 3222.035| |-----------------------------------------------------------------------------| r_work (start): 0.3722 rms_B_bonded: 2.13 r_work: 0.3601 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3481 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.2568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2830 Z= 0.143 Angle : 0.455 5.886 3815 Z= 0.237 Chirality : 0.048 0.124 505 Planarity : 0.001 0.004 480 Dihedral : 3.728 11.158 420 Min Nonbonded Distance : 2.639 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.20 % Allowed : 14.80 % Favored : 84.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.96 (0.38), residues: 340 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.01 (0.29), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.010 0.002 TYR M 39 PHE 0.002 0.001 PHE J 94 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.14 ( 2830) covalent geometry : angle 0.45478 / 0.24 ( 3815) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 680 Ramachandran restraints generated. 340 Oldfield, 0 Emsley, 340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 680 Ramachandran restraints generated. 340 Oldfield, 0 Emsley, 340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 42 time to evaluate : 0.069 Fit side-chains REVERT: A 32 LYS cc_start: 0.8080 (mttt) cc_final: 0.7736 (mtpt) REVERT: D 32 LYS cc_start: 0.8396 (mttt) cc_final: 0.7856 (mtpp) REVERT: G 32 LYS cc_start: 0.8135 (mttt) cc_final: 0.7806 (mtmt) REVERT: G 38 LEU cc_start: 0.9117 (OUTLIER) cc_final: 0.8760 (pp) REVERT: J 32 LYS cc_start: 0.8472 (mttt) cc_final: 0.7938 (mtpt) REVERT: J 42 SER cc_start: 0.9205 (p) cc_final: 0.8962 (p) REVERT: M 32 LYS cc_start: 0.8655 (mttt) cc_final: 0.8350 (mtmt) outliers start: 3 outliers final: 2 residues processed: 44 average time/residue: 0.4703 time to fit residues: 21.2134 Evaluate side-chains 44 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 41 time to evaluate : 0.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain G residue 38 LEU Chi-restraints excluded: chain J residue 38 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 17 optimal weight: 10.0000 chunk 23 optimal weight: 7.9990 chunk 29 optimal weight: 10.0000 chunk 32 optimal weight: 5.9990 chunk 9 optimal weight: 9.9990 chunk 21 optimal weight: 4.9990 chunk 16 optimal weight: 7.9990 chunk 6 optimal weight: 9.9990 chunk 12 optimal weight: 9.9990 chunk 24 optimal weight: 9.9990 chunk 26 optimal weight: 9.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... M 50 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.116479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.098521 restraints weight = 3243.279| |-----------------------------------------------------------------------------| r_work (start): 0.3673 rms_B_bonded: 2.08 r_work: 0.3556 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3436 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.2499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.045 2830 Z= 0.398 Angle : 0.723 7.097 3815 Z= 0.371 Chirality : 0.055 0.137 505 Planarity : 0.003 0.008 480 Dihedral : 4.712 14.654 420 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 2.80 % Allowed : 13.20 % Favored : 84.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.12 (0.37), residues: 340 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.13 (0.28), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.018 0.004 TYR G 39 PHE 0.004 0.001 PHE G 94 Details of bonding type rmsd/Z covalent geometry : bond 0.00863 / 0.40 ( 2830) covalent geometry : angle 0.72327 / 0.37 ( 3815) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 839.55 seconds wall clock time: 15 minutes 9.14 seconds (909.14 seconds total)