Starting phenix.real_space_refine on Fri Jul 3 04:13:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/10yb_75523/07_2026/10yb_75523.cif Found real_map, /net/cci-nas-00/data/ceres_data/10yb_75523/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/10yb_75523/07_2026/10yb_75523.map" default_real_map = "/net/cci-nas-00/data/ceres_data/10yb_75523/07_2026/10yb_75523.map" model { file = "/net/cci-nas-00/data/ceres_data/10yb_75523/07_2026/10yb_75523.cif" } default_model = "/net/cci-nas-00/data/ceres_data/10yb_75523/07_2026/10yb_75523.cif" } 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-dev-6108/lib/python3.11/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: 1.00 Conformation dependent library (CDL) restraints added in 241.5 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: 1.96 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: 2.52 Time building geometry restraints manager: 1.35 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=" C3' DA I 52 " pdb=" C2' DA I 52 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.18e+00 bond pdb=" C3' DT J 15 " pdb=" C2' DT J 15 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 8.90e+00 bond pdb=" C3' DG K 137 " pdb=" C2' DG K 137 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 8.68e+00 bond pdb=" C3' DC I 12 " pdb=" C2' DC I 12 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.58e+00 bond pdb=" C3' DG J 52 " pdb=" C2' DG J 52 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.45e+00 ... (remaining 12711 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.60: 17189 1.60 - 3.20: 1170 3.20 - 4.79: 55 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=" N3 DT J 50 " pdb=" C4 DT J 50 " pdb=" O4 DT J 50 " ideal model delta sigma weight residual 119.90 122.58 -2.68 6.00e-01 2.78e+00 2.00e+01 angle pdb=" N3 DT I 32 " pdb=" C4 DT I 32 " pdb=" O4 DT I 32 " ideal model delta sigma weight residual 119.90 122.53 -2.63 6.00e-01 2.78e+00 1.93e+01 angle pdb=" N3 DT I 31 " pdb=" C4 DT I 31 " pdb=" O4 DT I 31 " ideal model delta sigma weight residual 119.90 122.53 -2.63 6.00e-01 2.78e+00 1.92e+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: 1452 0.043 - 0.087: 479 0.087 - 0.130: 156 0.130 - 0.174: 9 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: 6.500 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: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.870 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: 29.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8959 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 12716 Z= 0.550 Angle : 0.803 7.991 18437 Z= 0.697 Chirality : 0.047 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/Z covalent geometry : bond 0.00645 / 0.55 (12716) covalent geometry : angle 0.80337 / 0.70 (18437) hydrogen bonds : bond 0.10596 / 6.76 ( 773) hydrogen bonds : angle 4.31198 / 3.00 ( 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 : 0.361 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: 0.9652 time to fit residues: 150.3135 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 : 0.322 ------------------------------------------------------------------------------- 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: 20.0000 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: 4.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 chunk 45 optimal weight: 3.9990 overall best weight: 0.9190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3575 r_free = 0.3575 target = 0.097753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.062634 restraints weight = 23100.325| |-----------------------------------------------------------------------------| r_work (start): 0.2889 rms_B_bonded: 1.53 r_work: 0.2712 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work: 0.2579 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8904 moved from start: 0.0530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12716 Z= 0.162 Angle : 0.629 6.619 18437 Z= 0.380 Chirality : 0.046 0.225 2100 Planarity : 0.004 0.036 1313 Dihedral : 30.728 144.337 4034 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.95 % Allowed : 16.72 % Favored : 81.33 % 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: 2.27 (0.31), residues: 726 helix: 2.16 (0.22), residues: 549 sheet: None (None), residues: 0 loop : -0.60 (0.42), residues: 177 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 79 TYR 0.013 0.001 TYR H 42 PHE 0.012 0.001 PHE A 67 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.16 (12716) covalent geometry : angle 0.62886 / 0.38 (18437) hydrogen bonds : bond 0.04935 / 3.34 ( 773) hydrogen bonds : angle 3.32715 / 2.31 ( 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 159 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 147 time to evaluate : 0.406 Fit side-chains REVERT: A 59 GLU cc_start: 0.8383 (mt-10) cc_final: 0.8132 (mt-10) REVERT: B 78 ARG cc_start: 0.9102 (mtm-85) cc_final: 0.8682 (mtm-85) REVERT: C 15 LYS cc_start: 0.8409 (ptpp) cc_final: 0.8149 (ptmm) REVERT: C 73 ASN cc_start: 0.9028 (t0) cc_final: 0.8485 (t0) REVERT: E 59 GLU cc_start: 0.8469 (pt0) cc_final: 0.8056 (pm20) REVERT: E 79 LYS cc_start: 0.8548 (tttt) cc_final: 0.8295 (tttp) REVERT: E 115 LYS cc_start: 0.9262 (OUTLIER) cc_final: 0.8903 (mtpt) REVERT: G 64 GLU cc_start: 0.8570 (OUTLIER) cc_final: 0.8192 (tp30) REVERT: G 73 ASN cc_start: 0.8845 (t0) cc_final: 0.8630 (t160) outliers start: 12 outliers final: 3 residues processed: 152 average time/residue: 0.9623 time to fit residues: 154.0242 Evaluate side-chains 148 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 143 time to evaluate : 0.327 ------------------------------------------------------------------------------- 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 64 GLU 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: 3.9990 chunk 53 optimal weight: 5.9990 chunk 14 optimal weight: 4.9990 chunk 0 optimal weight: 8.9990 chunk 65 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 chunk 12 optimal weight: 3.9990 chunk 23 optimal weight: 0.6980 chunk 49 optimal weight: 2.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.097177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.061994 restraints weight = 23336.238| |-----------------------------------------------------------------------------| r_work (start): 0.2914 rms_B_bonded: 1.53 r_work: 0.2740 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work: 0.2610 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8937 moved from start: 0.0616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 12716 Z= 0.193 Angle : 0.624 5.922 18437 Z= 0.373 Chirality : 0.045 0.243 2100 Planarity : 0.004 0.037 1313 Dihedral : 30.868 144.669 4034 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 2.27 % Allowed : 16.72 % 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: 2.52 (0.31), residues: 726 helix: 2.37 (0.22), residues: 549 sheet: None (None), residues: 0 loop : -0.62 (0.42), residues: 177 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 0.012 0.001 PHE A 67 HIS 0.006 0.001 HIS D 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.19 (12716) covalent geometry : angle 0.62400 / 0.37 (18437) hydrogen bonds : bond 0.04666 / 3.17 ( 773) hydrogen bonds : angle 3.18312 / 2.21 ( 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 157 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 143 time to evaluate : 0.394 Fit side-chains REVERT: A 59 GLU cc_start: 0.8431 (mt-10) cc_final: 0.8164 (mt-10) REVERT: A 120 MET cc_start: 0.8634 (mtt) cc_final: 0.8426 (mtt) REVERT: B 93 GLN cc_start: 0.8718 (mt0) cc_final: 0.8509 (mm-40) REVERT: C 15 LYS cc_start: 0.8431 (ptpp) cc_final: 0.8158 (ptmm) REVERT: C 73 ASN cc_start: 0.9056 (t0) cc_final: 0.8524 (t0) REVERT: E 59 GLU cc_start: 0.8479 (pt0) cc_final: 0.8081 (pm20) REVERT: E 122 LYS cc_start: 0.8906 (OUTLIER) cc_final: 0.8688 (ptpt) REVERT: G 64 GLU cc_start: 0.8609 (OUTLIER) cc_final: 0.8223 (tp30) REVERT: G 73 ASN cc_start: 0.8898 (t0) cc_final: 0.8675 (t160) outliers start: 14 outliers final: 6 residues processed: 144 average time/residue: 0.9820 time to fit residues: 148.7454 Evaluate side-chains 148 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 140 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain D residue 63 ASN Chi-restraints excluded: chain D residue 122 THR 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: 10.0000 chunk 8 optimal weight: 1.9990 chunk 53 optimal weight: 4.9990 chunk 83 optimal weight: 30.0000 chunk 11 optimal weight: 0.5980 chunk 57 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 73 optimal weight: 10.0000 chunk 91 optimal weight: 9.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3568 r_free = 0.3568 target = 0.097304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.062221 restraints weight = 23118.920| |-----------------------------------------------------------------------------| r_work (start): 0.2927 rms_B_bonded: 1.51 r_work: 0.2754 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work: 0.2620 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8958 moved from start: 0.0716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 12716 Z= 0.173 Angle : 0.604 6.330 18437 Z= 0.366 Chirality : 0.043 0.211 2100 Planarity : 0.004 0.062 1313 Dihedral : 30.925 145.045 4034 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.46 % Allowed : 17.53 % 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: 2.66 (0.31), residues: 726 helix: 2.48 (0.22), residues: 547 sheet: None (None), residues: 0 loop : -0.57 (0.42), residues: 179 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 78 TYR 0.011 0.001 TYR C 57 PHE 0.011 0.001 PHE A 67 HIS 0.003 0.001 HIS D 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.17 (12716) covalent geometry : angle 0.60417 / 0.37 (18437) hydrogen bonds : bond 0.04478 / 3.05 ( 773) hydrogen bonds : angle 3.10052 / 2.15 ( 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 152 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 143 time to evaluate : 0.335 Fit side-chains REVERT: A 120 MET cc_start: 0.8609 (mtt) cc_final: 0.8381 (mtt) REVERT: B 93 GLN cc_start: 0.8686 (mt0) cc_final: 0.8475 (mm-40) REVERT: C 15 LYS cc_start: 0.8478 (ptpp) cc_final: 0.8202 (ptmm) REVERT: C 73 ASN cc_start: 0.9068 (t0) cc_final: 0.8518 (t0) REVERT: E 59 GLU cc_start: 0.8495 (pt0) cc_final: 0.8122 (pm20) REVERT: G 73 ASN cc_start: 0.8908 (t0) cc_final: 0.8677 (t160) outliers start: 9 outliers final: 5 residues processed: 145 average time/residue: 0.9772 time to fit residues: 148.9985 Evaluate side-chains 146 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 141 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain D residue 63 ASN Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 107 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 45 optimal weight: 0.7980 chunk 61 optimal weight: 4.9990 chunk 19 optimal weight: 0.1980 chunk 80 optimal weight: 9.9990 chunk 42 optimal weight: 4.9990 chunk 95 optimal weight: 10.0000 chunk 85 optimal weight: 30.0000 chunk 83 optimal weight: 30.0000 chunk 74 optimal weight: 10.9990 chunk 82 optimal weight: 10.9990 chunk 78 optimal weight: 10.0000 overall best weight: 4.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3515 r_free = 0.3515 target = 0.094171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.058315 restraints weight = 23313.032| |-----------------------------------------------------------------------------| r_work (start): 0.2843 rms_B_bonded: 1.63 r_work: 0.2666 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work: 0.2537 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8996 moved from start: 0.1245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.066 12716 Z= 0.354 Angle : 0.722 6.774 18437 Z= 0.405 Chirality : 0.049 0.235 2100 Planarity : 0.005 0.044 1313 Dihedral : 31.679 146.928 4034 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.27 % Allowed : 17.37 % Favored : 80.36 % 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: 2.30 (0.31), residues: 726 helix: 2.27 (0.22), residues: 549 sheet: None (None), residues: 0 loop : -0.93 (0.41), residues: 177 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 71 TYR 0.015 0.002 TYR D 42 PHE 0.016 0.003 PHE A 67 HIS 0.009 0.002 HIS D 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00774 / 0.35 (12716) covalent geometry : angle 0.72246 / 0.40 (18437) hydrogen bonds : bond 0.05846 / 3.97 ( 773) hydrogen bonds : angle 3.14698 / 2.18 ( 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 152 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 138 time to evaluate : 0.266 Fit side-chains REVERT: A 97 GLU cc_start: 0.8685 (OUTLIER) cc_final: 0.8461 (mt-10) REVERT: C 15 LYS cc_start: 0.8561 (ptpp) cc_final: 0.8271 (ptmm) REVERT: C 73 ASN cc_start: 0.9065 (t0) cc_final: 0.8513 (t0) REVERT: E 59 GLU cc_start: 0.8612 (pt0) cc_final: 0.8244 (pm20) REVERT: G 64 GLU cc_start: 0.8742 (OUTLIER) cc_final: 0.8265 (tp30) outliers start: 14 outliers final: 9 residues processed: 142 average time/residue: 1.0042 time to fit residues: 149.7423 Evaluate side-chains 144 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 133 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 GLU 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 Chi-restraints excluded: chain G residue 114 VAL 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: 0.6980 chunk 1 optimal weight: 0.5980 chunk 9 optimal weight: 0.7980 chunk 21 optimal weight: 0.7980 chunk 7 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 chunk 93 optimal weight: 10.0000 chunk 71 optimal weight: 30.0000 chunk 40 optimal weight: 2.9990 chunk 48 optimal weight: 0.9980 chunk 61 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 108 ASN A 113 HIS B 25 ASN C 104 GLN G 104 GLN G 110 ASN H 63 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.096632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.061132 restraints weight = 23176.575| |-----------------------------------------------------------------------------| r_work (start): 0.2905 rms_B_bonded: 1.53 r_work: 0.2731 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work: 0.2602 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8941 moved from start: 0.1200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 12716 Z= 0.139 Angle : 0.607 6.148 18437 Z= 0.358 Chirality : 0.044 0.276 2100 Planarity : 0.004 0.043 1313 Dihedral : 31.576 145.986 4034 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 2.11 % Allowed : 19.16 % Favored : 78.73 % 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: 2.78 (0.32), residues: 726 helix: 2.55 (0.22), residues: 549 sheet: None (None), residues: 0 loop : -0.50 (0.43), residues: 177 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 71 TYR 0.014 0.001 TYR H 40 PHE 0.007 0.001 PHE A 67 HIS 0.006 0.001 HIS D 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.14 (12716) covalent geometry : angle 0.60678 / 0.36 (18437) hydrogen bonds : bond 0.03886 / 2.64 ( 773) hydrogen bonds : angle 2.92173 / 2.03 ( 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 160 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 147 time to evaluate : 0.323 Fit side-chains REVERT: B 93 GLN cc_start: 0.8726 (mm-40) cc_final: 0.8499 (mp10) REVERT: C 15 LYS cc_start: 0.8540 (ptpp) cc_final: 0.8242 (ptmm) REVERT: C 73 ASN cc_start: 0.9040 (t0) cc_final: 0.8490 (t0) REVERT: E 59 GLU cc_start: 0.8492 (OUTLIER) cc_final: 0.8134 (pm20) REVERT: E 120 MET cc_start: 0.8676 (OUTLIER) cc_final: 0.8215 (mtt) REVERT: G 64 GLU cc_start: 0.8647 (OUTLIER) cc_final: 0.8208 (tp30) outliers start: 13 outliers final: 4 residues processed: 150 average time/residue: 0.9497 time to fit residues: 149.9809 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 : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain B residue 30 THR 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 120 MET Chi-restraints excluded: chain G residue 64 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 25 optimal weight: 4.9990 chunk 46 optimal weight: 2.9990 chunk 85 optimal weight: 30.0000 chunk 57 optimal weight: 2.9990 chunk 27 optimal weight: 4.9990 chunk 49 optimal weight: 0.5980 chunk 56 optimal weight: 0.9990 chunk 90 optimal weight: 10.0000 chunk 58 optimal weight: 0.8980 chunk 84 optimal weight: 30.0000 chunk 92 optimal weight: 10.0000 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 104 GLN G 104 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.096062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.060784 restraints weight = 23064.553| |-----------------------------------------------------------------------------| r_work (start): 0.2887 rms_B_bonded: 1.50 r_work: 0.2714 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work: 0.2586 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8946 moved from start: 0.1265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 12716 Z= 0.180 Angle : 0.614 6.617 18437 Z= 0.361 Chirality : 0.043 0.278 2100 Planarity : 0.004 0.042 1313 Dihedral : 31.538 145.917 4034 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.95 % Allowed : 19.64 % 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: 2.86 (0.32), residues: 726 helix: 2.62 (0.22), residues: 549 sheet: None (None), residues: 0 loop : -0.49 (0.44), residues: 177 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 71 TYR 0.012 0.001 TYR C 57 PHE 0.012 0.001 PHE A 67 HIS 0.005 0.001 HIS D 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.18 (12716) covalent geometry : angle 0.61383 / 0.36 (18437) hydrogen bonds : bond 0.04142 / 2.82 ( 773) hydrogen bonds : angle 2.89981 / 2.01 ( 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 155 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 143 time to evaluate : 0.335 Fit side-chains REVERT: B 93 GLN cc_start: 0.8720 (mm-40) cc_final: 0.8468 (mp10) REVERT: C 15 LYS cc_start: 0.8573 (ptpp) cc_final: 0.8262 (ptmm) REVERT: C 56 GLU cc_start: 0.8932 (OUTLIER) cc_final: 0.8554 (tt0) REVERT: C 73 ASN cc_start: 0.9048 (t0) cc_final: 0.8488 (t0) REVERT: E 59 GLU cc_start: 0.8507 (pt0) cc_final: 0.8164 (pm20) outliers start: 12 outliers final: 6 residues processed: 148 average time/residue: 0.9466 time to fit residues: 147.5956 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 : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 63 ASN 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: 0.7980 chunk 28 optimal weight: 0.5980 chunk 76 optimal weight: 10.0000 chunk 73 optimal weight: 10.0000 chunk 19 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 60 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 58 optimal weight: 0.8980 chunk 33 optimal weight: 0.8980 chunk 8 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 104 GLN G 104 GLN G 110 ASN H 63 ASN H 109 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.096681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.061350 restraints weight = 22920.567| |-----------------------------------------------------------------------------| r_work (start): 0.2908 rms_B_bonded: 1.50 r_work: 0.2735 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work: 0.2608 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8938 moved from start: 0.1261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 12716 Z= 0.143 Angle : 0.602 6.702 18437 Z= 0.357 Chirality : 0.043 0.283 2100 Planarity : 0.004 0.041 1313 Dihedral : 31.528 145.764 4034 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % 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: 2.94 (0.32), residues: 726 helix: 2.68 (0.22), residues: 547 sheet: None (None), residues: 0 loop : -0.46 (0.43), residues: 179 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 71 TYR 0.012 0.001 TYR H 40 PHE 0.010 0.001 PHE A 67 HIS 0.007 0.001 HIS D 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.14 (12716) covalent geometry : angle 0.60197 / 0.36 (18437) hydrogen bonds : bond 0.03892 / 2.65 ( 773) hydrogen bonds : angle 2.88246 / 2.01 ( 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 153 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 144 time to evaluate : 0.336 Fit side-chains REVERT: B 93 GLN cc_start: 0.8687 (mm-40) cc_final: 0.8444 (mp10) REVERT: C 15 LYS cc_start: 0.8572 (ptpp) cc_final: 0.8259 (ptmm) REVERT: C 56 GLU cc_start: 0.8911 (OUTLIER) cc_final: 0.8529 (tt0) REVERT: C 73 ASN cc_start: 0.9039 (t0) cc_final: 0.8470 (t0) REVERT: E 59 GLU cc_start: 0.8486 (OUTLIER) cc_final: 0.8150 (pm20) outliers start: 9 outliers final: 4 residues processed: 146 average time/residue: 0.9693 time to fit residues: 148.8702 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 : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain C residue 56 GLU 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 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: 0.9990 chunk 12 optimal weight: 0.7980 chunk 84 optimal weight: 30.0000 chunk 34 optimal weight: 1.9990 chunk 31 optimal weight: 0.4980 chunk 33 optimal weight: 0.8980 chunk 69 optimal weight: 0.5980 chunk 64 optimal weight: 2.9990 chunk 96 optimal weight: 20.0000 chunk 97 optimal weight: 30.0000 chunk 48 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3563 r_free = 0.3563 target = 0.096948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.061841 restraints weight = 22929.603| |-----------------------------------------------------------------------------| r_work (start): 0.2911 rms_B_bonded: 1.49 r_work: 0.2741 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.2611 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8935 moved from start: 0.1309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 12716 Z= 0.141 Angle : 0.602 8.674 18437 Z= 0.355 Chirality : 0.043 0.290 2100 Planarity : 0.004 0.041 1313 Dihedral : 31.492 145.666 4034 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.30 % Allowed : 20.45 % 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: 2.99 (0.32), residues: 726 helix: 2.72 (0.22), residues: 547 sheet: None (None), residues: 0 loop : -0.43 (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 H 40 PHE 0.009 0.001 PHE A 67 HIS 0.002 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.14 (12716) covalent geometry : angle 0.60224 / 0.36 (18437) hydrogen bonds : bond 0.03733 / 2.54 ( 773) hydrogen bonds : angle 2.85895 / 2.00 ( 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 151 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 143 time to evaluate : 0.335 Fit side-chains REVERT: A 59 GLU cc_start: 0.8386 (OUTLIER) cc_final: 0.8057 (pm20) REVERT: B 93 GLN cc_start: 0.8691 (mm-40) cc_final: 0.8454 (mp10) REVERT: C 15 LYS cc_start: 0.8581 (ptpp) cc_final: 0.8266 (ptmm) REVERT: C 56 GLU cc_start: 0.8912 (OUTLIER) cc_final: 0.8531 (tt0) REVERT: C 73 ASN cc_start: 0.9046 (t0) cc_final: 0.8480 (t0) REVERT: E 59 GLU cc_start: 0.8479 (pt0) cc_final: 0.8119 (pm20) outliers start: 8 outliers final: 3 residues processed: 146 average time/residue: 0.9688 time to fit residues: 148.6842 Evaluate side-chains 146 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 141 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 63 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 1 optimal weight: 2.9990 chunk 94 optimal weight: 10.0000 chunk 56 optimal weight: 0.4980 chunk 50 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 88 optimal weight: 10.0000 chunk 31 optimal weight: 0.6980 chunk 63 optimal weight: 1.9990 chunk 19 optimal weight: 0.3980 chunk 26 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3569 r_free = 0.3569 target = 0.097317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.062150 restraints weight = 23169.632| |-----------------------------------------------------------------------------| r_work (start): 0.2917 rms_B_bonded: 1.49 r_work: 0.2747 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work: 0.2618 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8945 moved from start: 0.1298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 12716 Z= 0.137 Angle : 0.592 10.224 18437 Z= 0.353 Chirality : 0.043 0.293 2100 Planarity : 0.004 0.040 1313 Dihedral : 31.443 145.544 4034 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.30 % Allowed : 20.45 % 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: 2.76 (0.22), residues: 547 sheet: None (None), residues: 0 loop : -0.40 (0.44), residues: 179 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG G 71 TYR 0.012 0.001 TYR H 40 PHE 0.009 0.001 PHE A 67 HIS 0.008 0.001 HIS D 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.14 (12716) covalent geometry : angle 0.59247 / 0.35 (18437) hydrogen bonds : bond 0.03658 / 2.49 ( 773) hydrogen bonds : angle 2.83807 / 1.99 ( 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: 8 poor density : 144 time to evaluate : 0.340 Fit side-chains REVERT: A 59 GLU cc_start: 0.8382 (OUTLIER) cc_final: 0.8060 (pm20) REVERT: B 93 GLN cc_start: 0.8693 (mm-40) cc_final: 0.8483 (mp10) REVERT: C 15 LYS cc_start: 0.8611 (ptpp) cc_final: 0.8182 (ptmm) REVERT: C 56 GLU cc_start: 0.8927 (OUTLIER) cc_final: 0.8552 (tt0) REVERT: C 73 ASN cc_start: 0.9052 (t0) cc_final: 0.8481 (t0) REVERT: E 59 GLU cc_start: 0.8477 (OUTLIER) cc_final: 0.8142 (pm20) outliers start: 8 outliers final: 3 residues processed: 147 average time/residue: 0.9677 time to fit residues: 149.5767 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 : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 63 ASN Chi-restraints excluded: chain E residue 59 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 77 optimal weight: 10.0000 chunk 55 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 chunk 69 optimal weight: 4.9990 chunk 23 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 chunk 89 optimal weight: 10.0000 chunk 31 optimal weight: 4.9990 chunk 51 optimal weight: 0.0370 overall best weight: 2.2066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3547 r_free = 0.3547 target = 0.095933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.060588 restraints weight = 23125.525| |-----------------------------------------------------------------------------| r_work (start): 0.2890 rms_B_bonded: 1.51 r_work: 0.2717 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work: 0.2589 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8961 moved from start: 0.1378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 12716 Z= 0.210 Angle : 0.633 9.114 18437 Z= 0.367 Chirality : 0.044 0.297 2100 Planarity : 0.004 0.041 1313 Dihedral : 31.568 145.806 4034 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % 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: 2.95 (0.32), residues: 726 helix: 2.71 (0.22), residues: 547 sheet: None (None), residues: 0 loop : -0.54 (0.43), residues: 179 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 20 TYR 0.012 0.001 TYR C 57 PHE 0.012 0.002 PHE A 67 HIS 0.004 0.001 HIS D 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00433 / 0.21 (12716) covalent geometry : angle 0.63315 / 0.37 (18437) hydrogen bonds : bond 0.04290 / 2.91 ( 773) hydrogen bonds : angle 2.89016 / 2.02 ( 1925) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4783.59 seconds wall clock time: 82 minutes 13.53 seconds (4933.53 seconds total)