Starting phenix.real_space_refine on Sun Apr 5 16:56:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/10yb_75523/04_2026/10yb_75523.cif Found real_map, /net/cci-nas-00/data/ceres_data/10yb_75523/04_2026/10yb_75523.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/10yb_75523/04_2026/10yb_75523.cif" } default_model = "/net/cci-nas-00/data/ceres_data/10yb_75523/04_2026/10yb_75523.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/10yb_75523/04_2026/10yb_75523.map" default_real_map = "/net/cci-nas-00/data/ceres_data/10yb_75523/04_2026/10yb_75523.map" } resolution = 2.8 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= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 294 5.49 5 S 10 5.16 5 C 6568 2.51 5 N 2225 2.21 5 O 2807 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11904 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 789 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "B" Number of atoms: 622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 622 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "C" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 823 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "D" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 719 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "E" Number of atoms: 789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 789 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "F" Number of atoms: 633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 633 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain: "G" Number of atoms: 793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 793 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 5, 'TRANS': 97} Chain: "H" Number of atoms: 708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 708 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "I" Number of atoms: 2996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 2996 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "J" Number of atoms: 1155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 1155 Classifications: {'DNA': 56} Link IDs: {'rna3p': 55} Chain: "K" Number of atoms: 1877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 1877 Classifications: {'DNA': 91} Modifications used: {'p5*END': 1} Link IDs: {'rna3p': 90} Time building chain proxies: 2.63, per 1000 atoms: 0.22 Number of scatterers: 11904 At special positions: 0 Unit cell: (74.328, 123.88, 117.36, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 10 16.00 P 294 15.00 O 2807 8.00 N 2225 7.00 C 6568 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: 0.97 Conformation dependent library (CDL) restraints added in 347.0 milliseconds 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1384 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 9 sheets defined 74.5% alpha, 2.7% beta 147 base pairs and 262 stacking pairs defined. Time for finding SS restraints: 2.68 Creating SS restraints... Processing helix chain 'A' and resid 44 through 49 Processing helix chain 'A' and resid 50 through 57 removed outlier: 3.772A pdb=" N LYS A 56 " --> pdb=" O ARG A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 76 Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.626A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ARG B 55 " --> pdb=" O TYR B 51 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 27 through 36 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.383A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU C 65 " --> pdb=" O GLU C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'D' and resid 37 through 49 removed outlier: 3.543A pdb=" N GLN D 47 " --> pdb=" O LYS D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 84 Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 104 through 123 removed outlier: 3.514A pdb=" N LYS D 116 " --> pdb=" O SER D 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 42 through 57 removed outlier: 4.209A pdb=" N VAL E 46 " --> pdb=" O ARG E 42 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N ALA E 47 " --> pdb=" O PRO E 43 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 79 removed outlier: 3.527A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N PHE E 78 " --> pdb=" O ILE E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.793A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.525A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLN F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.351A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 89 Processing helix chain 'G' and resid 90 through 97 removed outlier: 3.511A pdb=" N LYS G 95 " --> pdb=" O GLU G 91 " (cutoff:3.500A) Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 Processing helix chain 'H' and resid 90 through 102 Processing helix chain 'H' and resid 104 through 124 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.300A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 removed outlier: 6.667A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.341A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.036A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA8, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.291A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'G' and resid 77 through 78 397 hydrogen bonds defined for protein. 1173 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 376 hydrogen bonds 752 hydrogen bond angles 0 basepair planarities 147 basepair parallelities 262 stacking parallelities Total time for adding SS restraints: 2.40 Time building geometry restraints manager: 1.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2053 1.33 - 1.45: 4259 1.45 - 1.57: 5798 1.57 - 1.68: 586 1.68 - 1.80: 20 Bond restraints: 12716 Sorted by residual: bond pdb=" C ARG A 42 " pdb=" N PRO A 43 " ideal model delta sigma weight residual 1.333 1.362 -0.029 1.01e-02 9.80e+03 8.03e+00 bond pdb=" N ILE F 26 " pdb=" CA ILE F 26 " ideal model delta sigma weight residual 1.459 1.492 -0.033 1.30e-02 5.92e+03 6.51e+00 bond pdb=" N ASN F 25 " pdb=" CA ASN F 25 " ideal model delta sigma weight residual 1.456 1.490 -0.034 1.35e-02 5.49e+03 6.36e+00 bond pdb=" N TYR A 41 " pdb=" CA TYR A 41 " ideal model delta sigma weight residual 1.456 1.487 -0.030 1.22e-02 6.72e+03 6.18e+00 bond pdb=" N ASN D 63 " pdb=" CA ASN D 63 " ideal model delta sigma weight residual 1.459 1.487 -0.028 1.19e-02 7.06e+03 5.59e+00 ... (remaining 12711 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.60: 17798 1.60 - 3.20: 581 3.20 - 4.79: 35 4.79 - 6.39: 16 6.39 - 7.99: 7 Bond angle restraints: 18437 Sorted by residual: angle pdb=" N VAL A 117 " pdb=" CA VAL A 117 " pdb=" C VAL A 117 " ideal model delta sigma weight residual 112.96 108.39 4.57 1.00e+00 1.00e+00 2.09e+01 angle pdb=" N LEU H 106 " pdb=" CA LEU H 106 " pdb=" C LEU H 106 " ideal model delta sigma weight residual 111.33 105.87 5.46 1.21e+00 6.83e-01 2.04e+01 angle pdb=" CB GLU C 91 " pdb=" CG GLU C 91 " pdb=" CD GLU C 91 " ideal model delta sigma weight residual 112.60 119.86 -7.26 1.70e+00 3.46e-01 1.83e+01 angle pdb=" C GLN E 76 " pdb=" CA GLN E 76 " pdb=" CB GLN E 76 " ideal model delta sigma weight residual 110.79 104.06 6.73 1.66e+00 3.63e-01 1.65e+01 angle pdb=" CA GLU C 91 " pdb=" CB GLU C 91 " pdb=" CG GLU C 91 " ideal model delta sigma weight residual 114.10 121.66 -7.56 2.00e+00 2.50e-01 1.43e+01 ... (remaining 18432 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.56: 5022 28.56 - 57.12: 1700 57.12 - 85.68: 152 85.68 - 114.24: 1 114.24 - 142.81: 3 Dihedral angle restraints: 6878 sinusoidal: 4730 harmonic: 2148 Sorted by residual: dihedral pdb=" CD ARG A 40 " pdb=" NE ARG A 40 " pdb=" CZ ARG A 40 " pdb=" NH1 ARG A 40 " ideal model delta sinusoidal sigma weight residual 0.00 -49.68 49.68 1 1.00e+01 1.00e-02 3.39e+01 dihedral pdb=" CA GLU A 50 " pdb=" C GLU A 50 " pdb=" N ILE A 51 " pdb=" CA ILE A 51 " ideal model delta harmonic sigma weight residual 180.00 160.58 19.42 0 5.00e+00 4.00e-02 1.51e+01 dihedral pdb=" C4' DG K 82 " pdb=" C3' DG K 82 " pdb=" O3' DG K 82 " pdb=" P DT K 83 " ideal model delta sinusoidal sigma weight residual 220.00 77.19 142.81 1 3.50e+01 8.16e-04 1.41e+01 ... (remaining 6875 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 1667 0.043 - 0.087: 357 0.087 - 0.130: 66 0.130 - 0.174: 6 0.174 - 0.217: 4 Chirality restraints: 2100 Sorted by residual: chirality pdb=" CA GLN E 76 " pdb=" N GLN E 76 " pdb=" C GLN E 76 " pdb=" CB GLN E 76 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.18e+00 chirality pdb=" CB THR H 119 " pdb=" CA THR H 119 " pdb=" OG1 THR H 119 " pdb=" CG2 THR H 119 " both_signs ideal model delta sigma weight residual False 2.55 2.34 0.21 2.00e-01 2.50e+01 1.07e+00 chirality pdb=" CA PRO H 103 " pdb=" N PRO H 103 " pdb=" C PRO H 103 " pdb=" CB PRO H 103 " both_signs ideal model delta sigma weight residual False 2.72 2.54 0.18 2.00e-01 2.50e+01 8.16e-01 ... (remaining 2097 not shown) Planarity restraints: 1313 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 40 " -0.848 9.50e-02 1.11e+02 3.80e-01 8.78e+01 pdb=" NE ARG A 40 " 0.049 2.00e-02 2.50e+03 pdb=" CZ ARG A 40 " 0.014 2.00e-02 2.50e+03 pdb=" NH1 ARG A 40 " 0.000 2.00e-02 2.50e+03 pdb=" NH2 ARG A 40 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP B 24 " 0.013 2.00e-02 2.50e+03 2.69e-02 7.24e+00 pdb=" C ASP B 24 " -0.047 2.00e-02 2.50e+03 pdb=" O ASP B 24 " 0.018 2.00e-02 2.50e+03 pdb=" N ASN B 25 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU F 63 " -0.010 2.00e-02 2.50e+03 2.06e-02 4.25e+00 pdb=" C GLU F 63 " 0.036 2.00e-02 2.50e+03 pdb=" O GLU F 63 " -0.013 2.00e-02 2.50e+03 pdb=" N ASN F 64 " -0.012 2.00e-02 2.50e+03 ... (remaining 1310 not shown) Histogram of nonbonded interaction distances: 2.54 - 3.01: 5773 3.01 - 3.48: 11374 3.48 - 3.96: 24290 3.96 - 4.43: 27157 4.43 - 4.90: 35310 Nonbonded interactions: 103904 Sorted by model distance: nonbonded pdb=" O ASP B 24 " pdb=" OD1 ASP B 24 " model vdw 2.540 3.040 nonbonded pdb=" O5' DA I 124 " pdb=" O4' DA I 124 " model vdw 2.542 2.432 nonbonded pdb=" N ILE G 79 " pdb=" O ILE G 79 " model vdw 2.580 2.496 nonbonded pdb=" N ILE C 79 " pdb=" O ILE C 79 " model vdw 2.589 2.496 nonbonded pdb=" N1 DG K 120 " pdb=" C4 DG K 120 " model vdw 2.592 2.672 ... (remaining 103899 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 24 through 101) } ncs_group { reference = (chain 'C' and resid 15 through 117) selection = chain 'G' } ncs_group { reference = (chain 'D' and resid 34 through 124) selection = chain 'H' } 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: 5.670 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: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.610 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8782 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 12716 Z= 0.230 Angle : 0.648 7.991 18437 Z= 0.396 Chirality : 0.038 0.217 2100 Planarity : 0.012 0.380 1313 Dihedral : 28.466 142.806 5494 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 0.49 % Allowed : 19.32 % Favored : 80.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.37 (0.30), residues: 726 helix: 1.52 (0.22), residues: 536 sheet: None (None), residues: 0 loop : -0.77 (0.40), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG D 33 TYR 0.015 0.002 TYR H 40 PHE 0.009 0.001 PHE C 25 HIS 0.005 0.001 HIS H 109 Details of bonding type rmsd covalent geometry : bond 0.00479 (12716) covalent geometry : angle 0.64808 (18437) hydrogen bonds : bond 0.10596 ( 773) hydrogen bonds : angle 4.31198 ( 1925) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 147 time to evaluate : 0.337 Fit side-chains REVERT: A 59 GLU cc_start: 0.8375 (mt-10) cc_final: 0.8171 (mt-10) REVERT: B 78 ARG cc_start: 0.9145 (mtm-85) cc_final: 0.8809 (mtm-85) REVERT: C 15 LYS cc_start: 0.8401 (ptpp) cc_final: 0.8132 (ptmm) REVERT: C 73 ASN cc_start: 0.9060 (t0) cc_final: 0.8520 (t0) REVERT: E 59 GLU cc_start: 0.8542 (pt0) cc_final: 0.8196 (pm20) REVERT: E 79 LYS cc_start: 0.8882 (tttt) cc_final: 0.8616 (tttp) REVERT: G 73 ASN cc_start: 0.8932 (t0) cc_final: 0.8707 (t160) outliers start: 3 outliers final: 0 residues processed: 148 average time/residue: 0.9272 time to fit residues: 144.1497 Evaluate side-chains 144 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 144 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 8.9990 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 0.0010 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 chunk 45 optimal weight: 3.9990 overall best weight: 0.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 GLN E 39 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.097993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.062807 restraints weight = 23173.633| |-----------------------------------------------------------------------------| r_work (start): 0.2939 rms_B_bonded: 1.55 r_work: 0.2764 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work: 0.2629 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.2629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8771 moved from start: 0.0477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 12716 Z= 0.163 Angle : 0.564 6.727 18437 Z= 0.341 Chirality : 0.034 0.235 2100 Planarity : 0.004 0.035 1313 Dihedral : 30.655 142.773 4034 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 1.95 % Allowed : 16.88 % Favored : 81.17 % 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: 2.28 (0.31), residues: 726 helix: 2.16 (0.22), residues: 549 sheet: None (None), residues: 0 loop : -0.58 (0.42), residues: 177 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 71 TYR 0.013 0.001 TYR H 42 PHE 0.013 0.001 PHE A 67 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00352 (12716) covalent geometry : angle 0.56380 (18437) hydrogen bonds : bond 0.04190 ( 773) hydrogen bonds : angle 3.26696 ( 1925) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 148 time to evaluate : 0.301 Fit side-chains REVERT: A 59 GLU cc_start: 0.8381 (mt-10) cc_final: 0.8139 (mt-10) REVERT: C 15 LYS cc_start: 0.8466 (ptpp) cc_final: 0.8207 (ptmm) REVERT: C 73 ASN cc_start: 0.9053 (t0) cc_final: 0.8511 (t0) REVERT: E 59 GLU cc_start: 0.8488 (pt0) cc_final: 0.8105 (pm20) REVERT: E 79 LYS cc_start: 0.8605 (tttt) cc_final: 0.8364 (tttp) REVERT: E 115 LYS cc_start: 0.9280 (OUTLIER) cc_final: 0.8924 (mtpt) REVERT: G 73 ASN cc_start: 0.8878 (t0) cc_final: 0.8662 (t160) outliers start: 12 outliers final: 3 residues processed: 153 average time/residue: 0.9390 time to fit residues: 150.8354 Evaluate side-chains 146 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 142 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 63 ASN Chi-restraints excluded: chain E residue 115 LYS Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 107 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 29 optimal weight: 2.9990 chunk 57 optimal weight: 4.9990 chunk 53 optimal weight: 4.9990 chunk 14 optimal weight: 4.9990 chunk 0 optimal weight: 7.9990 chunk 65 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 21 optimal weight: 0.8980 chunk 12 optimal weight: 3.9990 chunk 23 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 GLN G 104 GLN G 110 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.097445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.062334 restraints weight = 23366.956| |-----------------------------------------------------------------------------| r_work (start): 0.2921 rms_B_bonded: 1.52 r_work: 0.2749 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work: 0.2620 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8777 moved from start: 0.0536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 12716 Z= 0.199 Angle : 0.560 6.048 18437 Z= 0.337 Chirality : 0.034 0.235 2100 Planarity : 0.004 0.058 1313 Dihedral : 30.607 143.390 4034 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.79 % Allowed : 17.21 % Favored : 81.01 % 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: 2.49 (0.31), residues: 726 helix: 2.35 (0.22), residues: 547 sheet: None (None), residues: 0 loop : -0.62 (0.42), residues: 179 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 79 TYR 0.010 0.001 TYR C 57 PHE 0.011 0.001 PHE A 67 HIS 0.006 0.001 HIS D 109 Details of bonding type rmsd covalent geometry : bond 0.00446 (12716) covalent geometry : angle 0.55982 (18437) hydrogen bonds : bond 0.04056 ( 773) hydrogen bonds : angle 3.12959 ( 1925) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 141 time to evaluate : 0.312 Fit side-chains REVERT: A 59 GLU cc_start: 0.8415 (mt-10) cc_final: 0.8166 (mt-10) REVERT: C 15 LYS cc_start: 0.8437 (ptpp) cc_final: 0.8170 (ptmm) REVERT: C 73 ASN cc_start: 0.9065 (t0) cc_final: 0.8527 (t0) REVERT: E 59 GLU cc_start: 0.8484 (pt0) cc_final: 0.8098 (pm20) REVERT: E 122 LYS cc_start: 0.8925 (OUTLIER) cc_final: 0.8701 (ptpt) REVERT: G 64 GLU cc_start: 0.8603 (OUTLIER) cc_final: 0.8229 (tp30) REVERT: G 73 ASN cc_start: 0.8891 (t0) cc_final: 0.8660 (t160) outliers start: 11 outliers final: 4 residues processed: 142 average time/residue: 0.9790 time to fit residues: 145.9073 Evaluate side-chains 146 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 140 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain D residue 63 ASN Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain G residue 114 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 94 optimal weight: 4.9990 chunk 8 optimal weight: 1.9990 chunk 53 optimal weight: 4.9990 chunk 83 optimal weight: 10.0000 chunk 11 optimal weight: 0.9980 chunk 57 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 chunk 62 optimal weight: 0.9980 chunk 73 optimal weight: 4.9990 chunk 91 optimal weight: 3.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 GLN G 104 GLN G 110 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.096536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.061282 restraints weight = 23179.217| |-----------------------------------------------------------------------------| r_work (start): 0.2906 rms_B_bonded: 1.54 r_work: 0.2730 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work: 0.2600 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8772 moved from start: 0.0741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 12716 Z= 0.258 Angle : 0.571 5.795 18437 Z= 0.344 Chirality : 0.036 0.235 2100 Planarity : 0.004 0.039 1313 Dihedral : 30.655 144.454 4034 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.44 % Allowed : 15.75 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.67 (0.32), residues: 726 helix: 2.49 (0.22), residues: 549 sheet: None (None), residues: 0 loop : -0.61 (0.43), residues: 177 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG G 71 TYR 0.012 0.002 TYR C 57 PHE 0.015 0.002 PHE A 67 HIS 0.007 0.001 HIS D 109 Details of bonding type rmsd covalent geometry : bond 0.00588 (12716) covalent geometry : angle 0.57142 (18437) hydrogen bonds : bond 0.04003 ( 773) hydrogen bonds : angle 3.01745 ( 1925) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 143 time to evaluate : 0.313 Fit side-chains REVERT: C 15 LYS cc_start: 0.8416 (ptpp) cc_final: 0.8135 (ptmm) REVERT: C 73 ASN cc_start: 0.9055 (t0) cc_final: 0.8507 (t0) REVERT: E 59 GLU cc_start: 0.8485 (pt0) cc_final: 0.8099 (pm20) REVERT: G 64 GLU cc_start: 0.8645 (OUTLIER) cc_final: 0.8236 (tp30) REVERT: G 73 ASN cc_start: 0.8880 (t0) cc_final: 0.8666 (t160) outliers start: 15 outliers final: 8 residues processed: 147 average time/residue: 0.9831 time to fit residues: 151.5849 Evaluate side-chains 150 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 141 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 63 ASN Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 76 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 45 optimal weight: 0.9980 chunk 61 optimal weight: 4.9990 chunk 19 optimal weight: 0.0170 chunk 80 optimal weight: 4.9990 chunk 42 optimal weight: 0.7980 chunk 95 optimal weight: 4.9990 chunk 85 optimal weight: 8.9990 chunk 83 optimal weight: 7.9990 chunk 74 optimal weight: 5.9990 chunk 82 optimal weight: 5.9990 chunk 78 optimal weight: 4.9990 overall best weight: 2.3622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 GLN D 109 HIS G 104 GLN G 110 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.095812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.060409 restraints weight = 23251.621| |-----------------------------------------------------------------------------| r_work (start): 0.2888 rms_B_bonded: 1.53 r_work: 0.2713 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work: 0.2584 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8783 moved from start: 0.1018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 12716 Z= 0.260 Angle : 0.571 5.447 18437 Z= 0.344 Chirality : 0.036 0.162 2100 Planarity : 0.004 0.041 1313 Dihedral : 30.897 145.374 4034 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.79 % Allowed : 17.05 % Favored : 81.17 % 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: 2.74 (0.32), residues: 726 helix: 2.54 (0.22), residues: 549 sheet: None (None), residues: 0 loop : -0.58 (0.43), residues: 177 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 79 TYR 0.012 0.002 TYR C 57 PHE 0.012 0.002 PHE A 67 HIS 0.005 0.001 HIS D 109 Details of bonding type rmsd covalent geometry : bond 0.00595 (12716) covalent geometry : angle 0.57139 (18437) hydrogen bonds : bond 0.04013 ( 773) hydrogen bonds : angle 2.92760 ( 1925) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 142 time to evaluate : 0.306 Fit side-chains REVERT: A 59 GLU cc_start: 0.8493 (mt-10) cc_final: 0.8272 (mt-10) REVERT: C 15 LYS cc_start: 0.8481 (ptpp) cc_final: 0.8193 (ptmm) REVERT: C 73 ASN cc_start: 0.9049 (t0) cc_final: 0.8600 (t0) REVERT: C 75 LYS cc_start: 0.9054 (OUTLIER) cc_final: 0.8506 (mtpp) REVERT: E 59 GLU cc_start: 0.8522 (pt0) cc_final: 0.8171 (pm20) REVERT: G 64 GLU cc_start: 0.8686 (OUTLIER) cc_final: 0.8256 (tp30) REVERT: G 73 ASN cc_start: 0.9004 (t0) cc_final: 0.8794 (t160) REVERT: G 92 GLU cc_start: 0.8791 (OUTLIER) cc_final: 0.8572 (mt-10) outliers start: 11 outliers final: 6 residues processed: 146 average time/residue: 0.9555 time to fit residues: 146.5452 Evaluate side-chains 149 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 140 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain C residue 75 LYS Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 63 ASN Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain H residue 116 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 46 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 9 optimal weight: 0.0010 chunk 21 optimal weight: 0.9980 chunk 7 optimal weight: 2.9990 chunk 33 optimal weight: 0.6980 chunk 93 optimal weight: 4.9990 chunk 71 optimal weight: 7.9990 chunk 40 optimal weight: 0.5980 chunk 48 optimal weight: 0.6980 chunk 61 optimal weight: 3.9990 overall best weight: 0.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN A 113 HIS C 104 GLN G 104 GLN G 110 ASN H 63 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.097328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.062043 restraints weight = 23202.196| |-----------------------------------------------------------------------------| r_work (start): 0.2914 rms_B_bonded: 1.53 r_work: 0.2741 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work: 0.2611 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.2611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8754 moved from start: 0.1045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 12716 Z= 0.146 Angle : 0.541 5.773 18437 Z= 0.330 Chirality : 0.034 0.223 2100 Planarity : 0.004 0.039 1313 Dihedral : 30.911 144.788 4034 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 1.79 % Allowed : 18.99 % Favored : 79.22 % 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: 2.89 (0.32), residues: 726 helix: 2.61 (0.22), residues: 549 sheet: None (None), residues: 0 loop : -0.39 (0.44), residues: 177 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 71 TYR 0.012 0.001 TYR C 57 PHE 0.007 0.001 PHE A 67 HIS 0.003 0.001 HIS D 109 Details of bonding type rmsd covalent geometry : bond 0.00311 (12716) covalent geometry : angle 0.54070 (18437) hydrogen bonds : bond 0.03394 ( 773) hydrogen bonds : angle 2.83985 ( 1925) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 148 time to evaluate : 0.322 Fit side-chains REVERT: C 15 LYS cc_start: 0.8460 (ptpp) cc_final: 0.8166 (ptmm) REVERT: C 73 ASN cc_start: 0.9039 (t0) cc_final: 0.8579 (t0) REVERT: C 75 LYS cc_start: 0.9028 (OUTLIER) cc_final: 0.8455 (mtpp) REVERT: E 59 GLU cc_start: 0.8468 (OUTLIER) cc_final: 0.8126 (pm20) outliers start: 11 outliers final: 5 residues processed: 151 average time/residue: 0.9423 time to fit residues: 149.4462 Evaluate side-chains 150 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 143 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain C residue 75 LYS Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 63 ASN Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain H residue 116 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 25 optimal weight: 5.9990 chunk 46 optimal weight: 0.8980 chunk 85 optimal weight: 8.9990 chunk 57 optimal weight: 2.9990 chunk 27 optimal weight: 4.9990 chunk 49 optimal weight: 0.5980 chunk 56 optimal weight: 0.6980 chunk 90 optimal weight: 4.9990 chunk 58 optimal weight: 0.9990 chunk 84 optimal weight: 10.0000 chunk 92 optimal weight: 5.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 GLN G 104 GLN G 110 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.097136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.061807 restraints weight = 23100.758| |-----------------------------------------------------------------------------| r_work (start): 0.2874 rms_B_bonded: 1.52 r_work: 0.2697 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work: 0.2564 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8737 moved from start: 0.1130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 12716 Z= 0.179 Angle : 0.544 6.773 18437 Z= 0.331 Chirality : 0.033 0.161 2100 Planarity : 0.004 0.038 1313 Dihedral : 30.803 144.918 4034 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.79 % Allowed : 19.97 % Favored : 78.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.05 (0.32), residues: 726 helix: 2.73 (0.22), residues: 549 sheet: None (None), residues: 0 loop : -0.37 (0.44), residues: 177 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG G 71 TYR 0.012 0.001 TYR C 57 PHE 0.011 0.001 PHE A 67 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00399 (12716) covalent geometry : angle 0.54446 (18437) hydrogen bonds : bond 0.03464 ( 773) hydrogen bonds : angle 2.76806 ( 1925) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 145 time to evaluate : 0.307 Fit side-chains REVERT: A 59 GLU cc_start: 0.8466 (mt-10) cc_final: 0.8182 (mp0) REVERT: C 15 LYS cc_start: 0.8449 (ptpp) cc_final: 0.8150 (ptmm) REVERT: C 73 ASN cc_start: 0.9037 (t0) cc_final: 0.8568 (t0) REVERT: C 75 LYS cc_start: 0.9026 (OUTLIER) cc_final: 0.8459 (mtpp) REVERT: E 59 GLU cc_start: 0.8489 (OUTLIER) cc_final: 0.8124 (pm20) REVERT: G 92 GLU cc_start: 0.8782 (mt-10) cc_final: 0.8518 (mt-10) outliers start: 11 outliers final: 5 residues processed: 151 average time/residue: 0.9668 time to fit residues: 153.1240 Evaluate side-chains 148 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 141 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain C residue 75 LYS Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 63 ASN Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain H residue 116 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 18 optimal weight: 0.5980 chunk 28 optimal weight: 0.7980 chunk 76 optimal weight: 4.9990 chunk 73 optimal weight: 5.9990 chunk 19 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 60 optimal weight: 0.5980 chunk 14 optimal weight: 0.8980 chunk 58 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 8 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 GLN G 104 GLN G 110 ASN H 63 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.097489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.062288 restraints weight = 22932.405| |-----------------------------------------------------------------------------| r_work (start): 0.2923 rms_B_bonded: 1.51 r_work: 0.2751 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work: 0.2621 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8766 moved from start: 0.1170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 12716 Z= 0.158 Angle : 0.546 6.620 18437 Z= 0.331 Chirality : 0.033 0.217 2100 Planarity : 0.004 0.062 1313 Dihedral : 30.809 144.836 4034 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.46 % Allowed : 20.13 % Favored : 78.41 % 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: 3.13 (0.32), residues: 726 helix: 2.81 (0.22), residues: 547 sheet: None (None), residues: 0 loop : -0.35 (0.44), residues: 179 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 71 TYR 0.012 0.001 TYR H 40 PHE 0.010 0.001 PHE A 67 HIS 0.005 0.001 HIS D 109 Details of bonding type rmsd covalent geometry : bond 0.00345 (12716) covalent geometry : angle 0.54636 (18437) hydrogen bonds : bond 0.03307 ( 773) hydrogen bonds : angle 2.76598 ( 1925) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 146 time to evaluate : 0.246 Fit side-chains REVERT: C 15 LYS cc_start: 0.8503 (ptpp) cc_final: 0.8077 (ptmm) REVERT: C 73 ASN cc_start: 0.9059 (t0) cc_final: 0.8598 (t0) REVERT: C 75 LYS cc_start: 0.9070 (OUTLIER) cc_final: 0.8480 (mtpp) REVERT: E 59 GLU cc_start: 0.8468 (OUTLIER) cc_final: 0.8131 (pm20) outliers start: 9 outliers final: 4 residues processed: 150 average time/residue: 0.9333 time to fit residues: 147.0882 Evaluate side-chains 148 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 142 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain C residue 75 LYS Chi-restraints excluded: chain D residue 63 ASN Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain H residue 116 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 18 optimal weight: 0.7980 chunk 12 optimal weight: 0.6980 chunk 84 optimal weight: 10.0000 chunk 34 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 69 optimal weight: 0.9990 chunk 64 optimal weight: 2.9990 chunk 96 optimal weight: 6.9990 chunk 97 optimal weight: 10.0000 chunk 48 optimal weight: 0.7980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 GLN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 GLN G 110 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.097587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.062414 restraints weight = 23009.006| |-----------------------------------------------------------------------------| r_work (start): 0.2933 rms_B_bonded: 1.50 r_work: 0.2762 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work: 0.2633 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8765 moved from start: 0.1201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 12716 Z= 0.161 Angle : 0.550 9.125 18437 Z= 0.332 Chirality : 0.033 0.232 2100 Planarity : 0.004 0.054 1313 Dihedral : 30.785 144.769 4034 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.14 % Allowed : 20.62 % Favored : 78.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.16 (0.32), residues: 726 helix: 2.83 (0.22), residues: 547 sheet: None (None), residues: 0 loop : -0.34 (0.44), residues: 179 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 20 TYR 0.011 0.001 TYR H 40 PHE 0.009 0.001 PHE A 67 HIS 0.005 0.001 HIS D 109 Details of bonding type rmsd covalent geometry : bond 0.00355 (12716) covalent geometry : angle 0.54977 (18437) hydrogen bonds : bond 0.03223 ( 773) hydrogen bonds : angle 2.74905 ( 1925) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 145 time to evaluate : 0.287 Fit side-chains REVERT: A 59 GLU cc_start: 0.8446 (OUTLIER) cc_final: 0.8234 (mp0) REVERT: C 15 LYS cc_start: 0.8379 (ptpp) cc_final: 0.8139 (ptmm) REVERT: C 73 ASN cc_start: 0.9056 (t0) cc_final: 0.8506 (t0) REVERT: E 59 GLU cc_start: 0.8467 (OUTLIER) cc_final: 0.8134 (pm20) outliers start: 7 outliers final: 3 residues processed: 147 average time/residue: 0.9618 time to fit residues: 148.1992 Evaluate side-chains 147 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 142 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain D residue 63 ASN Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 87 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 1 optimal weight: 0.8980 chunk 94 optimal weight: 5.9990 chunk 56 optimal weight: 4.9990 chunk 50 optimal weight: 2.9990 chunk 9 optimal weight: 0.7980 chunk 5 optimal weight: 0.9990 chunk 88 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 19 optimal weight: 0.0770 chunk 26 optimal weight: 0.6980 overall best weight: 0.6940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 GLN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 GLN G 110 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.098018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.062737 restraints weight = 23257.081| |-----------------------------------------------------------------------------| r_work (start): 0.2944 rms_B_bonded: 1.53 r_work: 0.2772 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work: 0.2639 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8764 moved from start: 0.1230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12716 Z= 0.151 Angle : 0.546 10.933 18437 Z= 0.330 Chirality : 0.033 0.208 2100 Planarity : 0.004 0.040 1313 Dihedral : 30.746 144.633 4034 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 0.97 % Allowed : 20.94 % Favored : 78.08 % 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: 3.21 (0.31), residues: 726 helix: 2.86 (0.22), residues: 547 sheet: None (None), residues: 0 loop : -0.31 (0.44), residues: 179 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 20 TYR 0.011 0.001 TYR H 40 PHE 0.009 0.001 PHE A 67 HIS 0.004 0.001 HIS D 109 Details of bonding type rmsd covalent geometry : bond 0.00327 (12716) covalent geometry : angle 0.54640 (18437) hydrogen bonds : bond 0.03140 ( 773) hydrogen bonds : angle 2.72547 ( 1925) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 146 time to evaluate : 0.316 Fit side-chains REVERT: A 59 GLU cc_start: 0.8365 (OUTLIER) cc_final: 0.8158 (mp0) REVERT: A 97 GLU cc_start: 0.8471 (OUTLIER) cc_final: 0.8229 (mm-30) REVERT: C 15 LYS cc_start: 0.8416 (ptpp) cc_final: 0.8118 (ptmm) REVERT: C 73 ASN cc_start: 0.9056 (t0) cc_final: 0.8563 (t0) REVERT: E 59 GLU cc_start: 0.8455 (OUTLIER) cc_final: 0.8140 (pm20) outliers start: 6 outliers final: 3 residues processed: 148 average time/residue: 0.9583 time to fit residues: 148.9456 Evaluate side-chains 149 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 143 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain D residue 63 ASN Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 87 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 77 optimal weight: 4.9990 chunk 55 optimal weight: 2.9990 chunk 9 optimal weight: 0.1980 chunk 69 optimal weight: 4.9990 chunk 23 optimal weight: 0.9990 chunk 14 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 89 optimal weight: 4.9990 chunk 31 optimal weight: 4.9990 chunk 51 optimal weight: 4.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 GLN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 GLN G 110 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.097209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.061899 restraints weight = 23132.189| |-----------------------------------------------------------------------------| r_work (start): 0.2921 rms_B_bonded: 1.51 r_work: 0.2750 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work: 0.2616 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8779 moved from start: 0.1281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 12716 Z= 0.190 Angle : 0.562 9.700 18437 Z= 0.337 Chirality : 0.034 0.205 2100 Planarity : 0.004 0.037 1313 Dihedral : 30.778 144.743 4034 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.46 % Allowed : 20.45 % Favored : 78.08 % 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: 3.18 (0.32), residues: 726 helix: 2.85 (0.22), residues: 547 sheet: None (None), residues: 0 loop : -0.36 (0.44), residues: 179 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG G 71 TYR 0.012 0.001 TYR C 57 PHE 0.010 0.001 PHE A 67 HIS 0.005 0.001 HIS D 109 Details of bonding type rmsd covalent geometry : bond 0.00426 (12716) covalent geometry : angle 0.56228 (18437) hydrogen bonds : bond 0.03509 ( 773) hydrogen bonds : angle 2.74016 ( 1925) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4930.02 seconds wall clock time: 84 minutes 19.67 seconds (5059.67 seconds total)